Displaying publications 1 - 20 of 513 in total

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  1. Sirunyan AM, Tumasyan A, Adam W, Ambrogi F, Bergauer T, Dragicevic M, et al.
    Comput Softw Big Sci, 2020;4(1):10.
    PMID: 33196702 DOI: 10.1007/s41781-020-00041-z
    We describe a method to obtain point and dispersion estimates for the energies of jets arising from b quarks produced in proton-proton collisions at an energy of s = 13 TeV at the CERN LHC. The algorithm is trained on a large sample of simulated b jets and validated on data recorded by the CMS detector in 2017 corresponding to an integrated luminosity of 41 fb - 1 . A multivariate regression algorithm based on a deep feed-forward neural network employs jet composition and shape information, and the properties of reconstructed secondary vertices associated with the jet. The results of the algorithm are used to improve the sensitivity of analyses that make use of b jets in the final state, such as the observation of Higgs boson decay to b b ¯ .
  2. Alqasaimeh MS, Heng LY, Ahmad M
    Sensors (Basel), 2007 Oct 11;7(10):2251-2262.
    PMID: 28903225 DOI: 10.3390/s7102251
    An optical urea biosensor was fabricated by stacking several layers of sol-gelfilms. The stacking of the sol-gel films allowed the immobilization of a Nile Bluechromoionophore (ETH 5294) and urease enzyme separately without the need of anychemical attachment procedure. The absorbance response of the biosensor was monitoredat 550 nm, i.e. the deprotonation of the chromoionophore. This multi-layer sol-gel filmformat enabled higher enzyme loading in the biosensor to be achieved. The urea opticalbiosensor constructed from three layers of sol-gel films that contained urease demonstrateda much wider linear response range of up to 100 mM urea when compared with biosensorsthat constructed from 1-2 layers of films. Analysis of urea in urine samples with thisoptical urea biosensor yielded results similar to that determined by a spectrophotometricmethod using the reagent p-dimethylaminobenzaldehyde (R² = 0.982, n = 6). The averagerecovery of urea from urine samples using this urea biosensor is approximately 103%.
  3. Ahmad M, Jung LT, Bhuiyan AA
    Comput Methods Programs Biomed, 2017 Oct;149:11-17.
    PMID: 28802326 DOI: 10.1016/j.cmpb.2017.06.021
    BACKGROUND AND OBJECTIVE: Digital signal processing techniques commonly employ fixed length window filters to process the signal contents. DNA signals differ in characteristics from common digital signals since they carry nucleotides as contents. The nucleotides own genetic code context and fuzzy behaviors due to their special structure and order in DNA strand. Employing conventional fixed length window filters for DNA signal processing produce spectral leakage and hence results in signal noise. A biological context aware adaptive window filter is required to process the DNA signals.

    METHODS: This paper introduces a biological inspired fuzzy adaptive window median filter (FAWMF) which computes the fuzzy membership strength of nucleotides in each slide of window and filters nucleotides based on median filtering with a combination of s-shaped and z-shaped filters. Since coding regions cause 3-base periodicity by an unbalanced nucleotides' distribution producing a relatively high bias for nucleotides' usage, such fundamental characteristic of nucleotides has been exploited in FAWMF to suppress the signal noise.

    RESULTS: Along with adaptive response of FAWMF, a strong correlation between median nucleotides and the Π shaped filter was observed which produced enhanced discrimination between coding and non-coding regions contrary to fixed length conventional window filters. The proposed FAWMF attains a significant enhancement in coding regions identification i.e. 40% to 125% as compared to other conventional window filters tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms.

    CONCLUSION: This study proves that conventional fixed length window filters applied to DNA signals do not achieve significant results since the nucleotides carry genetic code context. The proposed FAWMF algorithm is adaptive and outperforms significantly to process DNA signal contents. The algorithm applied to variety of DNA datasets produced noteworthy discrimination between coding and non-coding regions contrary to fixed window length conventional filters.

  4. Ulianas A, Heng LY, Ahmad M
    Sensors (Basel), 2011;11(9):8323-38.
    PMID: 22164078 DOI: 10.3390/s110908323
    New acrylic microspheres were synthesised by photopolymerisation where the succinimide functional group was incorporated during the microsphere preparation. An optical biosensor for urea based on reflectance transduction with a large linear response range to urea was successfully developed using this material. The biosensor utilized succinimide-modified acrylic microspheres immobilized with a Nile blue chromoionophore (ETH 5294) for optical detection and urease enzyme was immobilized on the surface of the microspheres via the succinimide groups. No leaching of the enzyme or chromoionophore was observed. Hydrolysis of the urea by urease changes the pH and leads to a color change of the immobilized chromoionophore. When the color change was monitored by reflectance spectrophotometry, the linear response range of the biosensor to urea was from 0.01 to 1,000 mM (R2 = 0.97) with a limit of detection of 9.97 μM. The biosensor response showed good reproducibility (relative standard deviation = 1.43%, n = 5) with no interference by major cations such as Na+, K+, NH4+ and Mg2+. The use of reflectance as a transduction method led to a large linear response range that is better than that of many urea biosensors based on other optical transduction methods.
  5. Arip MN, Heng LY, Ahmad M, Ujang S
    Talanta, 2013 Nov 15;116:776-81.
    PMID: 24148473 DOI: 10.1016/j.talanta.2013.07.065
    The characteristics of a potentiometric biosensor for the determination of permethrin in treated wood based on immobilised cells of the fungus Lentinus sajor-caju on a potentiometric transducer are reported this paper. The potentiometric biosensor was prepared by immobilisation of the fungus in alginate gel deposited on a pH-sensitive transducer employing a photocurable acrylic matrix. The biosensor gave a good response in detecting permethrin over the range of 1.0-100.0 µM. The slope of the calibration curve was 56.10 mV/decade with detection limit of 1.00 µM. The relative standard deviation for the sensor reproducibility was 4.86%. The response time of the sensor was 5 min at optimum pH 8.0 with 1.00 mg/electrode of fungus L. sajor-caju. The permethrin biosensor performance was compared with the conventional method for permethrin analysis using high performance liquid chromatography (HPLC), and the analytical results agreed well with the HPLC method (at 95% confidence limit). There was no interference from commonly used organophosphorus pesticides such as diazinon, parathion, paraoxon, and methyl parathion.
  6. Majeed Butt O, Shakeel Ahmad M, Kai Lun T, Seng Che H, Fayaz H, Abd Rahim N, et al.
    Waste Manag, 2023 Feb 01;156:1-11.
    PMID: 36424243 DOI: 10.1016/j.wasman.2022.11.016
    The integration of hydrogen in the primary energy mix requires a major technological shift in virtually every energy-related application. This study has attempted to investigate the techno-economic solar photovoltaic (PV) integrated water electrolysis and waste incineration system. Three different strategies, i.e., (i) PV + Battery(Hybrid mode with required batteries); (ii) auto-ignition (Direct coupling); and (iii) PV + Secondary-Electrolyzer(Direct coupling assisted with secondary electrolyzer), have been envisioned. The 'PV + Battery' consume 42.42 % and 15.07 % less energy than the auto-ignition and 'PV + Secondary-Electrolyzer' methods. However, the capital cost of 'PV + Battery' has been calculated to be 15.4 % and 11.8 % more than auto-ignition and 'PV + Secondary-Electrolyzer, respectively.The energy consumption relative to waste input, the 'PV + Battery' method used 80 % less energy, while auto-ignition and 'PV + Secondary-Electrolyzer' showed 70.5 % and 77.5 % less energy, respectively. Furthermore, these approaches showed a vast difference in cost-benefit for the longer run. 'PV + Battery' was forecasted to be 73.3 % and 23.3 % more expensive than auto-ignition and 'PV + Secondary-Electrolyzer' methods, respectively, for 30 years. Overall, this study can benefit from using either of these methods depending on the application, usage scale, and climatic conditions.
  7. Yusof NA, Ahmad M
    Talanta, 2002 Sep 12;58(3):459-66.
    PMID: 18968772
    Gallocynin immobilized in chitosan membrane has been studied as a sensor element of an optical sensor for lead using a flowing system. By using this set up, lead in solution has been determined in the concentration range from 1.0x10(-1) to 1.0x10(3) ppm with a detection limit of 0.075 ppm. The standard deviation of the method for the repeatability of lead detection at a concentration of 100 ppm was found to be 2.10%. The response of the sensor was reproducible and can be regenerated by using acidified saturated KNO(3) solution. Interference from foreign ions was also studied at 1:1 mole ratio of Pb(II):foreign ions.
  8. Alqasaimeh M, Heng LY, Ahmad M, Raj AS, Ling TL
    Sensors (Basel), 2014 Jul 22;14(7):13186-209.
    PMID: 25054632 DOI: 10.3390/s140713186
    A new silica-gel nanospheres (SiO2NPs) composition was formulated, followed by biochemical surface functionalization to examine its potential in urea biosensor development. The SiO2NPs were basically synthesized based on sol-gel chemistry using a modified Stober method. The SiO2NPs surfaces were modified with amine (-NH2) functional groups for urease immobilization in the presence of glutaric acid (GA) cross-linker. The chromoionophore pH-sensitive dye ETH 5294 was physically adsorbed on the functionalized SiO2NPs as pH transducer. The immobilized urease determined urea concentration reflectometrically based on the colour change of the immobilized chromoionophore as a result of the enzymatic hydrolysis of urea. The pH changes on the biosensor due to the catalytic enzyme reaction of immobilized urease were found to correlate with the urea concentrations over a linear response range of 50-500 mM (R2 = 0.96) with a detection limit of 10 mM urea. The biosensor response time was 9 min with reproducibility of less than 10% relative standard deviation (RSD). This optical urea biosensor did not show interferences by Na+, K+, Mg2+ and NH4+ ions. The biosensor performance has been validated using urine samples in comparison with a non-enzymatic method based on the use of p-dimethylaminobenzaldehyde (DMAB) reagent and demonstrated a good correlation between the two different methods (R2 = 0.996 and regression slope of 1.0307). The SiO2NPs-based reflectometric urea biosensor showed improved dynamic linear response range when compared to other nanoparticle-based optical urea biosensors.
  9. Sirunyan AM, Tumasyan A, Adam W, Ambrogi F, Bergauer T, Brandstetter J, et al.
    Eur Phys J C Part Fields, 2020;80(3):237.
    PMID: 32215380 DOI: 10.1140/epjc/s10052-020-7773-5
    A search in an all-jet final state for new massive resonances decaying to W W , W Z , or Z Z boson pairs using a novel analysis method is presented. The analysis is performed on data corresponding to an integrated luminosity of 77.3 fb - 1 recorded with the CMS experiment at the LHC at a centre-of-mass energy of 13  Te . The search is focussed on potential narrow-width resonances with masses above 1.2  Te , where the decay products of each W or Z boson are expected to be collimated into a single, large-radius jet. The signal is extracted using a three-dimensional maximum likelihood fit of the two jet masses and the dijet invariant mass, yielding an improvement in sensitivity of up to 30% relative to previous search methods. No excess is observed above the estimated standard model background. In a heavy vector triplet model, spin-1 Z ' and W ' resonances with masses below 3.5 and 3.8   Te , respectively, are excluded at 95% confidence level. In a bulk graviton model, upper limits on cross sections are set between 27 and 0.2 fb for resonance masses between 1.2 and 5.2   Te , respectively. The limits presented in this paper are the best to date in the dijet final state.
  10. Magsi A, Mahar JA, Maitlo A, Ahmad M, Razzaq MA, Bhuiyan MAS, et al.
    Sci Rep, 2023 Sep 16;13(1):15381.
    PMID: 37717081 DOI: 10.1038/s41598-023-41727-9
    Date palm is an important domestic cash crop in most countries. Sudden Decline Syndrome (SDS) causes a huge loss to the crop both in quality and quantity. The literature reports the significance of early detection of disease towards preventive measures to improve the quality of the crop. The number of prevailing detection methods limits to consideration of a certain aspect of disease identification. This study proposes a new hybrid fuzzy fast multi-Otsu K-Means (FFMKO) algorithm integrating the date palm image enhancement, robust thresholding, and optimal clustering for significant disease identification. The algorithm adopts a multi-operator image resizing cost function based on image energy and the dominant color descriptor, the adaptive Fuzzy noise filter, and Otsu image thresholding combined with K-Means clustering enhancements. Besides, we validate the process with histogram equalization and threshold transformation towards enhanced color feature extraction of date palm images. The algorithm authenticates findings on a local dataset of 3293 date palm images and, on a benchmarked data set as well. It achieves an accuracy of 94.175% for successful detection of SDS that outperforms the existing similar algorithms. The impactful findings of this study assure the fast and authentic detection of the disease at an earlier stage to uplift the quality and quantity of the date palm and boost the agriculture-based economy.
  11. Omar B, Kurahashi H, Jeffery J, Yasohdha N, Lau SY, John MC, et al.
    Trop Biomed, 2007 Dec;24(2):99-100.
    PMID: 18209716
    Fannia pusio (Wiedemann) (Diptera: Fanniidae) is newly recorded from Malaysia. This record is based on 1male symbol 1female symbol from Sarawak, east Malaysia and 1male symbol 2female symbol from Selangor, peninsular Malaysia. It is included in the pusio group of Fannia wherein are included Fannia femoralis (Stein), Fannia howardi Malloch, Fannia trimaculata (Stein), Fannia leucosticta (Meigen) and Fannia punctiventris Malloch. The male of Fannia pusio is differentiated from other members of the group by the following features: hind femur with a swelling bearing a number of setae that are usually curled at tip; squamae creamy; tergite 1+2 broadly grey dusted at sides.
  12. Suah FB, Ahmad M, Heng LY
    PMID: 25748985 DOI: 10.1016/j.saa.2015.02.068
    A novel approach for the determination of Al(3+) from aqueous samples was developed using an optode membrane produced by physical inclusion of Al(3+) selective reagent, which is morin into a plasticized poly(vinyl chloride). The inclusion of Triton X-100 was found to be valuable and useful for enhancing the sorption of Al(3+) ions from liquid phase into the membrane phase, thus increasing the intensity of optode's absorption. The optode showed a linear increase in the absorbance at λ(max)=425 nm over the concentration range of 1.85×10(-6)-1.1×10(-4) mol L(-1) (0.05-3 μg mL(-1)) of Al(3+) ions in aqueous solution after 5 min. The limit of detection was determined to be 1.04×10(-6) mol L(-1) (0.028 μg mL(-1)). The optode developed in the present work was easily prepared and found to be stable, has good mechanical strength, sensitive and reusable. In addition, the optode was tested for Al(3+) determination in lake water, river water and pharmaceutical samples, which the result was satisfactory.
  13. Basuni M, Muhi J, Othman N, Verweij JJ, Ahmad M, Miswan N, et al.
    Am J Trop Med Hyg, 2011 Feb;84(2):338-43.
    PMID: 21292911 DOI: 10.4269/ajtmh.2011.10-0499
    Soil-transmitted helminth infections remain a major public health burden in low- and middle-income countries. The traditional diagnosis by microscopic examination of fecal samples is insensitive and time-consuming. In this study, a pentaplex real-time polymerase chain reaction (PCR) was evaluated for the simultaneous detection of Ancylostoma, Necator americanus, Ascaris lumbricoides, and Strongyloides stercoralis. The results were compared with those obtained by conventional parasitological diagnostic methods. Real-time PCR was positive in 48 of 77 samples (62.3%) and microscopic examination was positive in six samples (7.8%) only (P < 0.05). In conclusion, the real-time PCR assay described in this study provides a specific and sensitive diagnostic tool for the detection of these four helminth species in epidemiological studies and monitoring of treatment programs.
  14. Munir M, Ahmad M, Mubashir M, Asif S, Waseem A, Mukhtar A, et al.
    Bioresour Technol, 2021 May;328:124859.
    PMID: 33621759 DOI: 10.1016/j.biortech.2021.124859
    The potential of new trimetallic (Ce, Cu, La) loaded montmorillonite clay catalyst for synthesizing biodiesel using novel non-edible Celastrus paniculatus Willd seed oil via two-step transesterification reaction has been reported along with catalyst characterization. Transesterification reaction was optimized and maximum biodiesel yield of 89.42% achieved under optimal operating reaction states like; 1:12 oil to methanol ratio, 3.5% of catalyst amount, 120 °C of reaction temperature for 3 h. The predicted and experimental biodiesel yields under these reaction conditions were 89.42 and 89.40%, which showing less than 0.05% variation. Additionally, optimum biodiesel yield can be predicted by drawing 3D surface plots and 2D contour plots using MINITAB 17 software. For the characterization of the obtained biodiesel, analysis including the GC/MS, FT-IR, 1H NMR and 13C NMR were applied. The fuel properties of obtained biodiesel agrees well with the different European Union (EU-14214), China (GB/T 20828), and American (ASTM-951, 6751) standards.
  15. Soon CF, Thong KT, Tee KS, Ismail AB, Denyer M, Ahmad MK, et al.
    Biotech Histochem, 2016 May;91(4):283-95.
    PMID: 27008034 DOI: 10.3109/10520295.2016.1158865
    We describe a new scaffold-free three-dimensional (3D) cell culture model using cholesteryl ester based lyotropic liquid crystal (LC) substrates. Keratinocytes were deposited randomly on the LC surface where they self-assembled into 3D microtissues or keratinospheroids. The cell density required to form spheroids was optimized. We investigated cell viability using dead/live cell assays. The adhesion characteristics of cells within the microtissues were determined using histological sectioning and immunofluorescence staining. Fourier transform infrared spectroscopy (FTIR) was used to characterize the biochemistry of the keratinospheroids. We found that both cells and microtissues could migrate on the LC surface. The viability study indicated approximately 80% viability of cells in the microtissues up to 20 days of culture. Strong intercellular adhesion was observed in the stratification of the multi-layered microspheroids using field emission-scanning electron microscopy (FE-SEM) and histochemical staining. The cytoskeleton and vinculins of the cells in the microtissues were expressed diffusely, but the microtissues were enriched with lipids and nucleic acids, which indicates close resemblance to the conditions in vivo. The basic 3D culture model based on LC may be used for cell and microtissue migration studies in response to cytochemical treatment.
  16. Tumasyan A, Adam W, Andrejkovic JW, Bergauer T, Chatterjee S, Damanakis K, et al.
    Eur Phys J C Part Fields, 2023;83(10):933.
    PMID: 37855556 DOI: 10.1140/epjc/s10052-023-11952-7
    A search for decays to invisible particles of Higgs bosons produced in association with a top-antitop quark pair or a vector boson, which both decay to a fully hadronic final state, has been performed using proton-proton collision data collected at s=13TeV by the CMS experiment at the LHC, corresponding to an integrated luminosity of 138fb-1. The 95% confidence level upper limit set on the branching fraction of the 125GeV Higgs boson to invisible particles, B(H→inv), is 0.54 (0.39 expected), assuming standard model production cross sections. The results of this analysis are combined with previous B(H→inv) searches carried out at s=7, 8, and 13TeV in complementary production modes. The combined upper limit at 95% confidence level on B(H→inv) is 0.15 (0.08 expected).
  17. Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Asilar E, Bergauer T, et al.
    Eur Phys J C Part Fields, 2017;77(5):294.
    PMID: 28579921 DOI: 10.1140/epjc/s10052-017-4787-8
    A search for new phenomena is performed in final states containing one or more jets and an imbalance in transverse momentum in pp collisions at a centre-of-mass energy of 13[Formula: see text]. The analysed data sample, recorded with the CMS detector at the CERN LHC, corresponds to an integrated luminosity of 2.3[Formula: see text]. Several kinematic variables are employed to suppress the dominant background, multijet production, as well as to discriminate between other standard model and new physics processes. The search provides sensitivity to a broad range of new-physics models that yield a stable weakly interacting massive particle. The number of observed candidate events is found to agree with the expected contributions from standard model processes, and the result is interpreted in the mass parameter space of fourteen simplified supersymmetric models that assume the pair production of gluinos or squarks and a range of decay modes. For models that assume gluino pair production, masses up to 1575 and 975[Formula: see text] are excluded for gluinos and neutralinos, respectively. For models involving the pair production of top squarks and compressed mass spectra, top squark masses up to 400[Formula: see text] are excluded.
  18. Yam MF, Mohamed EA, Ang LF, Pei L, Darwis Y, Mahmud R, et al.
    J Acupunct Meridian Stud, 2012 Aug;5(4):176-82.
    PMID: 22898066 DOI: 10.1016/j.jams.2012.05.005
    Orthosiphon stamineus extracts contain three flavonoids (3'-hydroxy-5,6,7,4'-tetramethoxyflavone, sinensetin, and eupatorin) as bioactive substances. Previous reported high performance liquid chromatography- ultraviolet (HPLC-UV) methods for the determination of these flavonoids have several disadvantages, including unsatisfactory separation times and not being well validated according to International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) standard guidelines. A rapid, specific reversed-phase HPLC method with isocratic elution of acetonitrile: isopropyl alcohol: 20mM phosphate buffer (NaH(2)PO(4)) (30:15:55, v/v) (pH 3.5) at a flow-rate of 1ml/minute, a column temperature of 25°C, and ultraviolet (UV) detection at 340 nm was developed. The method was validated and applied for quantification of different types of O stamineus extracts and fractions. The method allowed simultaneous determination of 3'-hydroxy-5,6,7,4'-tetramethoxyflavone, sinensetin, and eupatorin in the concentration range of 0.03052-250 μg/ml. The limits of detection and quantification, respectively, were 0.0076 and 0.061 μg/ml for 3'-hydroxy-5,6,7,4'-tetramethoxyflavone, 0.0153 and 0.122 μg/ml for sinensetin and 0.0305 and 0.122 μg/ml for eupatorin. The percent relative standard deviation (% RSD) values for intraday were 0.048-0.368, 0.025-0.135, and 0.05-0.476 for 3'-hydroxy-5,6,7,4'-tetramethoxyflavone, sinensetin, and eupatorin, respectively, and those for intraday precision were 0.333-1.688, 0.722-1.055, and 0.548-1.819, respectively. The accuracy for intraday were 91.25%-103.38%, 94.32%-109.56%, and 92.85%-109.70% for 3'-hydroxy-5,6,7,4'-tetramethoxyflavone, sinensetin, and eupatorin, respectively, and those for interday accuracy were 97.49%-103.92%, 103.58%-104.57%, and 103.9%-105.33%, respectively. The method was found to be simple, accurate and precise and is recommended for routine quality control analysis of O stamineus extract containing the three flavonoids as the principle components in the extract.
  19. Kuswandi B, Irmawati T, Hidayat MA, Jayus, Ahmad M
    Sensors (Basel), 2014;14(2):2135-49.
    PMID: 24473284 DOI: 10.3390/s140202135
    A simple visual ethanol biosensor based on alcohol oxidase (AOX) immobilised onto polyaniline (PANI) film for halal verification of fermented beverage samples is described. This biosensor responds to ethanol via a colour change from green to blue, due to the enzymatic reaction of ethanol that produces acetaldehyde and hydrogen peroxide, when the latter oxidizes the PANI film. The procedure to obtain this biosensor consists of the immobilization of AOX onto PANI film by adsorption. For the immobilisation, an AOX solution is deposited on the PANI film and left at room temperature until dried (30 min). The biosensor was constructed as a dip stick for visual and simple use. The colour changes of the films have been scanned and analysed using image analysis software (i.e., ImageJ) to study the characteristics of the biosensor's response toward ethanol. The biosensor has a linear response in an ethanol concentration range of 0.01%-0.8%, with a correlation coefficient (r) of 0.996. The limit detection of the biosensor was 0.001%, with reproducibility (RSD) of 1.6% and a life time up to seven weeks when stored at 4 °C. The biosensor provides accurate results for ethanol determination in fermented drinks and was in good agreement with the standard method (gas chromatography) results. Thus, the biosensor could be used as a simple visual method for ethanol determination in fermented beverage samples that can be useful for Muslim community for halal verification.
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