Displaying publications 1 - 20 of 114 in total

  1. Yaeghoobi M, Rahman NA, Ng SW
    PMID: 21583886 DOI: 10.1107/S1600536809013348
    In the title Schiff base, C(16)H(16)ClNO(2), the 2-(4-methoxy-phen-yl)ethyl (CH(3)OC(6)H(4)CH(2)CH(2)-; r.m.s. deviation = 0.10 Å) and 4-chloro-2-(imino-meth-yl)phenol (N=CHC(6)H(3)ClOH; r.m.s. deviation = 0.01 Å) portions are both essentially planar, the two parts being inclined at an angle of 61.8 (1)°. The hydroxy group forms a hydrogen bond to the imino N atom.
  2. Ramanathan Y, Rajagopalan R, Rahman NA
    Ear Nose Throat J, 2007 Nov;86(11):685-6.
    PMID: 18225631
    Metastases to the larynx from distant primaries are rare. We report a case of a laryngeal metastasis from a rectal carcinoma.
  3. Asi AM, Rahman NA, Merican AF
    J. Mol. Graph. Model., 2004 Mar;22(4):249-62.
    PMID: 15177077
    Protein-ligand binding free energy values of wild-type and mutant C-terminal domain of Escherichia coli arginine repressor (ArgRc) protein systems bound to L-arginine or L-citrulline molecules were calculated using the linear interaction energy (LIE) method by molecular dynamics (MD) simulation. The binding behaviour predicted by the dissociation constant (K(d)) calculations from the binding free energy values showed preferences for binding of L-arginine to the wild-type ArgRc but not to the mutant ArgRc(D128N). On the other hand, L-citrulline do not favour binding to wild-type ArgRc but prefer binding to mutant ArgRc(D128N). The dissociation constant for the wild-type ArgRc-L-arginine complex obtained in this study is in agreement with reported experimental results. Our results also support the experimental data for the binding of L-citrulline to the mutant ArgRc(D128N). These showed that LIE method for protein-ligand binding free energy calculation could be applied to the wild-type and the mutant E. coli ArgRc-L-arginine and ArgRc-L-citrulline protein-ligand complexes and possibly to other transcriptional repressor-co-repressor systems as well.
  4. Kueh R, Rahman NA, Merican AF
    J Mol Model, 2003 Apr;9(2):88-98.
    PMID: 12707802
    The arginine repressor (ArgR) of Escherichia coli binds to six L-arginine molecules that act as its co-repressor in order to bind to DNA. The binding of L-arginine molecules as well as its structural analogues is compared by means of computational docking. A grid-based energy evaluation method combined with a Monte Carlo simulated annealing process was used in the automated docking. For all ligands, the docking procedure proposed more than one binding site in the C-terminal domain of ArgR (ArgRc). Interaction patterns of ArgRc with L-arginine were also observed for L-canavanine and L-citrulline. L-lysine and L-homoarginine, on the other hand, were shown to bind poorly at the binding site. Figure A general overview of the sites found from docking the various ligands into ArgRc ( grey ribbons). Red coloured sticks: residues in binding site H that was selected for docking
  5. Yusof AM, Rahman NA, Wood AK
    Biol Trace Elem Res, 1994;43-45:239-49.
    PMID: 7710833
    Trace elements, such as As, Co, Cr, Hg, Sb, and Zn, were determined by neutron activation analysis (NAA), whereas Cd, Cu, and Pb were determined by graphite furnace atomic absorption spectroscopy (GFAAS) in clam, crab, prawn, swamp cerith, and mussel samples after digestion by microwave heating under controlled conditions before eluting the solutions through a column of a chelating resin, Chelex-100. The standard used in the determination of percentage volatile elements retained by microwave digestion and also in the activation process was Lobster Hepatopancreas TORT-1, whereas known mixed standards were prepared from nitrate salts to determine the efficiency of the separation procedure at a controlled pH. Mercury and lead detected in crabs exceeded the maximum permissible level. Some species also showed a high affinity toward certain elements, and their levels of accumulation in the tissues of these species corresponded with the concentration of these elements in sediments, especially at sites in the vicinity of an industrial zone.
  6. Idris SS, Rahman NA, Ismail K
    Bioresour. Technol., 2012 Nov;123:581-91.
    PMID: 22944493 DOI: 10.1016/j.biortech.2012.07.065
    The combustion characteristics of Malaysia oil palm biomass (palm kernel shell (PKS), palm mesocarp fibre (PMF) and empty fruit bunches (EFB)), sub-bituminous coal (Mukah Balingian) and coal/biomass blends via thermogravimetric analysis (TGA) were investigated. Six weight ratios of coal/biomass blends were prepared and oxidised under dynamic conditions from temperature 25 to 1100°C at four heating rates. The thermogravimetric analysis demonstrated that the EFB and PKS evolved additional peak besides drying, devolatilisation and char oxidation steps during combustion. Ignition and burn out temperatures of blends were improved in comparison to coal. No interactions were observed between the coal and biomass during combustion. The apparent activation energy during this process was evaluated using iso-conversional model free kinetics which resulted in highest activation energy during combustion of PKS followed by PMF, EFB and MB coal. Blending oil palm biomass with coal reduces the apparent activation energy value.
  7. Othman S, Rahman NA, Yusof R
    Virus Res., 2012 Jan;163(1):238-45.
    PMID: 22001567 DOI: 10.1016/j.virusres.2011.09.040
    Despite aggressive efforts in dengue research, the control of dengue diseases and discovery of therapeutics against them await complete elucidation of its complex immune-pathogenesis. Unlike many viruses that escape the host's immune responses by suppressing the major histocompatibility complex (MHC) Class I pathway, many Flaviviruses up-regulate the cell surface expression of MHC Class I complex. We recently reported MHC Class I HLA-A2 promoter activation by all serotypes of dengue virus (DV). The mechanism by which DV regulates this is further explored here in HepG2 human liver cell line. Using real-time PCR, evidence that, similar to infections by other Flaviviruses, DV infection has the ability to up-regulate the MHC Class I transcription and mRNA synthesis, is presented. The region responsive towards DV infection of all serotypes was mapped to the Class I Regulatory Complex (CRC) of the HLA-A2 promoter. Competition electrophoretic mobility shift assay (EMSA) with NFκB probe established the presence of specific DNA-protein complex in DV-infected nuclear extracts. Antibody-supershift assays identified the MHC Class I promoter activation by DV to occur through binding of p65/p50 heterodimers and p65 homodimers to κB1 and κB2 cis-acting elements, respectively, within the CRC, and not with the interferon consensus sequence (ICS). This study presents evidence of MHC Class I gene modulation by DV, hence providing a better understanding of dengue immune-pathogenesis that would consequently facilitate the discovery of antiviral therapeutics against dengue.
  8. Kheng TY, Ding P, Abdul Rahman NA
    J. Sci. Food Agric., 2012 Jan 15;92(1):171-6.
    PMID: 21780132 DOI: 10.1002/jsfa.4559
    A series of physico-chemical quality (peel and pulp colours, pulp firmness, fruit pH, sugars and acids content, respiration rate and ethylene production) were conducted to study the optimum harvest periods (either week 11 or week 12 after emergence of the first hand) of Rastali banana (Musa AAB Rastali) based on the fruit quality during ripening.
  9. Othman S, Rahman NA, Yusof R
    Trans. R. Soc. Trop. Med. Hyg., 2010 Dec;104(12):806-8.
    PMID: 20800252 DOI: 10.1016/j.trstmh.2010.07.004
    In contrast to many viruses that escape the host's immune responses by suppressing the major histocompatibility complex (MHC) class I pathway, flaviviruses have been shown to up-regulate the cell surface expression of MHC class I complex. The mechanism by which dengue virus (DV) achieves this up-regulation remains unclear. Our investigation on the HLA-A2 gene in human liver cells demonstrated that all four serotypes of dengue virus, DV1 to DV4, resulted in variable degrees of promoter induction. This illustrates the importance of MHC class I transcription regulation in primary infections by different DV serotypes that may have even greater impact in secondary infections, associated with increased disease severity.
  10. Shamsul NS, Kamarudin SK, Rahman NA
    Bioresour. Technol., 2018 Jan;247:821-828.
    PMID: 30060418 DOI: 10.1016/j.biortech.2017.09.140
    Treated sludge, goat manure, sugarcane bagasse, empty fruit bunches of oil palm (EFBP) and dry leaves are agro wastes that have high potential for use as feedstocks for the production of 5-hydroxymethylfurfural (5-HMF). The focus of this study is to investigate the production of 5-HMF from agro wastes via co-hydrothermal (CHT) treatment and extraction. Present study include examine on agro waste's physical and chemical properties and also their thermal degradation behaviour. The analysis of the bio-oil products is conducted by FTIR and GC-MS. Co-hydrothermal experiments were conducted at a temperature of 300°C with an experimental time of 15min, followed by alcohol extraction. Highest carbon and hydrogen content are 45.94% and 6.49% (dry leaves) with maximum high heating value 18.39MJ/kg (dry leaves) and fix carbon value 6.60 (goat manure). Through CHT about 39% 5-HMF, 22.97% carboxylic acids, 0.97% of aromatic and 0.73% aldehyde obtained.
  11. Ahmed T, Rahman NA, Alam MK
    Eur J Dent, 2018 10 30;12(4):602-609.
    PMID: 30369810 DOI: 10.4103/ejd.ejd_22_18
    The aim of this study was to systematically review the available studies measuring the bond strength of orthodontic bracket-adhesive system under different experimental conditions in vivo. Literature search was performed in four different databases: PubMed, Web of Science, Cochrane, and Scopus using the keywords - bond strength, orthodontic brackets, bracket-adhesive, and in vivo. A total of six full-text articles were selected based on the inclusion and exclusion criteria of our study after a careful assessment by the two independent reviewers. Data selection was performed by following PRISMA 2009 guidelines. Five of the selected studies were clinical trials; one study was a randomized clinical trial. From each of the selected articles, the following data were extracted - number of samples, with the type of tooth involved materials under experiment methods of measurement, the time interval between bonding and debonding orthodontic brackets, mode of force application, and the bond strength results with the overall outcome. The methodological quality assessment of each article was done by the modified Downs and Black checklist method. The qualitative analyses were done by two independent reviewers. Conflicting issues were resolved in a consensus meeting by consulting the third reviewer (MKA). Meta-analysis could not be performed due to the lack of homogenous study results. The review reached no real conclusion apart from the lack of efforts to clinically evaluate the bonding efficiency of a wide range of orthodontic bracket-adhesive systems in terms of debonding force compared to laboratory-based in vitro and ex vivo studies.
  12. Roslan AA, Rahman NA, Alam MK
    J Orthod Sci, 2018;7:16.
    PMID: 30271761 DOI: 10.4103/jos.JOS_37_18
    OBJECTIVE: This study was carried to study the prevalence of dental anomalies and treatment modalities/planning among the orthodontic patients.

    MATERIALS AND METHODS: A total of 370 orthodontic records including their pre-treatment orthopantomographs (OPG) and study models of orthodontic patients in permanent dentition who attended dental clinic were assessed for impaction, hypodontia, supernumerary, supraocclusion, infraocclusion, and any other anomalies excluding the third molars. The association of anomalies with gender status and racial status was analyzed using Pearson's Chi-square test. A P value of <0.05 is considered as significant. The confidence interval at 95% (CI) was set.

    RESULTS: Among the 370 subjects, 105 (28.4%) presented with at least one anomaly. Eighty-five (23%) demonstrated a single anomaly and 20 (5.4%) with more than one anomaly. The most prevalent anomaly was impaction (14.32%), followed by hypodontia (7.03%). The less common anomalies were microdontia (1.08%), dilacerations (0.27%), and generalised enamel hypoplasia (0.27%). Maxillary right lateral incisors and canines were the most common affected teeth and these are located on the maxillary right quadrant. It was evident that dental anomalies were statistically dependant on race (P = 0.025), but independent of gender. The most common treatment planned for these patients was fixed appliance.

    CONCLUSIONS: Impaction was predominant among 28.4% subjects observed with anomaly and most patients with anomaly are treated with fixed appliances (49%).

    CLINICAL RELEVANCE: These anomalies play a great role in occlusion and alignment in treatment planning and relapse for orthodontic treatment.

  13. Ahmed T, Rahman NA, Alam MK
    Prog Orthod, 2019 Jul 08;20(1):26.
    PMID: 31281954 DOI: 10.1186/s40510-019-0277-x
    BACKGROUND: To introduce an orthodontic bracket debonding device capable of measuring debonding force clinically by a novel sensor mechanism MATERIALS AND METHOD: A prototype orthodontic debonding device was constructed utilizing a lift-off debonding instrument (LODI) and force-sensitive resistor (FSR). For data interpretation, the force sensor was equipped with a microcontroller and C++ programming software running on a computer. Ninety-nine (99) 0.022-in. conventional metallic brackets were bonded to premolar teeth in vitro by a single clinician applying the same adhesive and bonding technique. For validation, the mean debonding force measured by the prototype debonding device (n = 30) and the universal testing machine (n = 30) was compared. Both intra- and inter-examiner reliability tests were done by holding and operating the device in a standardized manner. Following debonding by the prototype device, the bracket failure pattern was evaluated (n = 30) by adhesive remnant index (ARI) under the stereomicroscope at × 30 magnification. Statistical analysis included independent samples t test for validation and intraclass correlation coefficient (ICC) with a 95% confidence interval for both intra- and inter-examiner reliability.

    RESULTS: Mean orthodontic bracket debonding force measured by the prototype device (9.36 ± 1.65 N) and the universal testing machine (10.43 ± 2.71 N) was not significantly different (p 

  14. Yaacob N, Mohamad Ali MS, Salleh AB, Abdul Rahman NA
    PeerJ, 2016;4:e1751.
    PMID: 26989608 DOI: 10.7717/peerj.1751
    Background. Not all yeast alcohol dehydrogenase 2 (ADH2) are repressed by glucose, as reported in Saccharomyces cerevisiae. Pichia stipitis ADH2 is regulated by oxygen instead of glucose, whereas Kluyveromyces marxianus ADH2 is regulated by neither glucose nor ethanol. For this reason, ADH2 regulation of yeasts may be species dependent, leading to a different type of expression and fermentation efficiency. Lachancea fermentati is a highly efficient ethanol producer, fast-growing cells and adapted to fermentation-related stresses such as ethanol and organic acid, but the metabolic information regarding the regulation of glucose and ethanol production is still lacking. Methods. Our investigation started with the stimulation of ADH2 activity from S. cerevisiae and L. fermentati by glucose and ethanol induction in a glucose-repressed medium. The study also embarked on the retrospective analysis of ADH2 genomic and protein level through direct sequencing and sites identification. Based on the sequence generated, we demonstrated ADH2 gene expression highlighting the conserved NAD(P)-binding domain in the context of glucose fermentation and ethanol production. Results. An increase of ADH2 activity was observed in starved L. fermentati (LfeADH2) and S. cerevisiae (SceADH2) in response to 2% (w/v) glucose induction. These suggest that in the presence of glucose, ADH2 activity was activated instead of being repressed. An induction of 0.5% (v/v) ethanol also increased LfeADH2 activity, promoting ethanol resistance, whereas accumulating acetic acid at a later stage of fermentation stimulated ADH2 activity and enhanced glucose consumption rates. The lack in upper stream activating sequence (UAS) and TATA elements hindered the possibility of Adr1 binding to LfeADH2. Transcription factors such as SP1 and RAP1 observed in LfeADH2 sequence have been implicated in the regulation of many genes including ADH2. In glucose fermentation, L. fermentati exhibited a bell-shaped ADH2 expression, showing the highest expression when glucose was depleted and ethanol-acetic acid was increased. Meanwhile, S. cerevisiae showed a constitutive ADH2 expression throughout the fermentation process. Discussion. ADH2 expression in L. fermentati may be subjected to changes in the presence of non-fermentative carbon source. The nucleotide sequence showed that ADH2 transcription could be influenced by other transcription genes of glycolysis oriented due to the lack of specific activation sites for Adr1. Our study suggests that if Adr1 is not capable of promoting LfeADH2 activation, the transcription can be controlled by Rap1 and Sp1 due to their inherent roles. Therefore in future, it is interesting to observe ADH2 gene being highly regulated by these potential transcription factors and functioned as a promoter for yeast under high volume of ethanol and organic acids.
  15. Hafid HS, Rahman NA, Md Shah UK, Baharudin AS
    J. Environ. Manage., 2015 Jun 1;156:290-8.
    PMID: 25900092 DOI: 10.1016/j.jenvman.2015.03.045
    The kitchen waste fraction in municipal solid waste contains high organic matter particularly carbohydrate that can contribute to fermentable sugar production for subsequent conversion to bioethanol. This study was carried out to evaluate the influence of single and combination pretreatments of kitchen waste by liquid hot water, mild acid pretreatment of hydrochloric acid (HCl) and sulphuric acid (H2SO4) and enzymatic hydrolysis (glucoamylase). The maximum total fermentable sugar produced after combination pretreatment by 1.5% HCl and glucoamylase consisted of 93.25 g/L glucose, 0.542 g/L sucrose, 0.348 g/L maltose, and 0.321 g/L fructose. The glucose released by the combination pretreatment method was 0.79 g glucose/g KW equivalent to 79% of glucose conversion. The effects of the pre-treatment on kitchen waste indicated that the highest solubilization was 40% by the combination method of 1.5% HCl and glucoamylase. The best combination pre-treatment gave concentrations of lactic acid, acetic acid, and propionic acid of 11.74 g/L, 6.77 g/L, and 1.02 g/L, respectively. The decrease of aliphatic absorbance bands of polysaccharides at 2851 and 2923 cm(-1) and the increase on structures of carbonyl absorbance bands at 1600 cm(-1) reflects the progress of the kitchen waste hydrolysis to fermentable sugars. Overall, 1.5% HCl and glucoamylase treatment was the most profitable process as the minimum selling price of glucose was USD 0.101/g kitchen waste. Therefore, the combination pretreatment method was proposed to enhance the production of fermentable sugar, particularly glucose from kitchen waste as the feedstock for bioethanol production.
  16. Ghazali N, Rahman NA, Kannan TP, Jaafar S
    Cleft Palate Craniofac. J., 2015 07;52(4):e88-94.
    PMID: 26151095 DOI: 10.1597/14-024
    OBJECTIVE: To determine the prevalence of mutations in transforming growth factor beta 3 (TGFβ3) and Jagged2 genes and their association with nonsyndromic cleft lip with or without cleft palate (CL±P) patients.

    DESIGN: Cross-sectional study on nonsyndromic CL±P and noncleft patients.

    SETTING: Reconstructive clinic and outpatient dental clinic, Hospital Universiti Sains Malaysia.

    PATIENTS: Blood samples of 96 nonsyndromic CL±P and 96 noncleft subjects.

    MAIN OUTCOME MEASURE: Prevalence and association of mutations in TGFβ3 and Jagged2 genes with nonsyndromic CL±P.

    RESULTS: Most of the nonsyndromic CL±P patients (53.1%) had left unilateral CLP. There were slightly more females (56.6%) compared with males. The prevalence of the mutations in the TGFβ3 gene was 17.7% (95% confidence interval [CI]: 9.5, 24.5) and in the Jagged2 gene was 12.5% (95% CI: 5.5, 18.5), which was higher compared with the noncleft group. For the TGFβ3 gene, there was no mutation in the coding region in either of the groups. All variants were single nucleotide polymorphisms located within the intronic flanking region. Two variants were identified (g.15812T>G and g.15966A>G) in both nonsyndromic CL±P and noncleft patients. However, the association was not significant (P > .05). Three variants (g.19779C>T, g.19547G>A, and g.19712C>T) were identified in the Jagged2 gene among nonsyndromic CL±P and noncleft patients. Only g.19712C>T showed a significant association with nonsyndromic CL±P patients (P = .039).

    CONCLUSION: g.19712C>T might play a crucial role in the development of cleft lip and palate. To the best of our knowledge, this is the first report of the mutation found within intron 13 of the Jagged2 gene among nonsyndromic CL±P Malay patients.

    Study site:Reconstructive and outpatient dental clinic, Hospital Universiti Sains Malaysia (HUSM)
  17. Rothan HA, Mohamed Z, Paydar M, Rahman NA, Yusof R
    Arch. Virol., 2014 Apr;159(4):711-8.
    PMID: 24142271 DOI: 10.1007/s00705-013-1880-7
    Doxycycline is an antibiotic derived from tetracycline that possesses antimicrobial and anti-inflammatory activities. Antiviral activity of doxycycline against dengue virus has been reported previously; however, its anti-dengue properties need further investigation. This study was conducted to determine the potential activity of doxycycline against dengue virus replication in vitro. Doxycycline inhibited the dengue virus serine protease (DENV2 NS2B-NS3pro) with an IC50 value of 52.3 ± 6.2 μM at 37 °C (normal human temperature) and 26.7 ± 5.3 μM at 40 °C (high fever temperature). The antiviral activity of doxycycline was first tested at different concentrations against DENV2 using a plaque-formation assay. The virus titter decreased significantly after applying doxycycline at levels lower than its 50 % cytotoxic concentration (CC50, 100 μM), showing concentration-dependent inhibition with a 50 % effective concentration (EC50) of approximately 50 μM. Doxycycline significantly inhibited viral entry and post-infection replication of the four dengue serotypes, with serotype-specific inhibition (high activity against DENV2 and DENV4 compared to DENV1 and DENV3). Collectively, these findings underline the need for further experimental and clinical studies on doxycycline, utilizing its anti-dengue and anti-inflammatory activities to attenuate the clinical symptoms of dengue virus infection.
  18. Othman R, Wahab HA, Yusof R, Rahman NA
    In Silico Biol. (Gedrukt), 2007;7(2):215-24.
    PMID: 17688447
    Multiple sequence alignment was performed against eight proteases from the Flaviviridae family using ClustalW to illustrate conserved domains. Two sets of prediction approaches were applied and the results compared. Firstly, secondary structure prediction was performed using available structure prediction servers. The second approach made use of the information on the secondary structures extracted from structure prediction servers, threading techniques and DSSP database of some of the templates used in the threading techniques. Consensus on the one-dimensional secondary structure of Den2 protease was obtained from each approach and evaluated against data from the recently crystallised Den2 NS2B/NS3 obtained from the Protein Data Bank (PDB). Results indicated the second approach to show higher accuracy compared to the use of prediction servers only. Thus, it is plausible that this approach is applicable to the initial stage of structural studies of proteins with low amino acid sequence homology against other available proteins in the PDB.
  19. Yehye WA, Ariffin A, Rahman NA, Ng SW
    PMID: 21583884 DOI: 10.1107/S1600536809013543
    The dianion of the title salt, 2C(5)H(6)N(+)·C(12)H(6)N(2)O(4)S(2) (2-), lies on a special position of 2 site symmetry that relates one thio-nicotinate part to the other, and the dihedral angle between the niotinate planes is 89.2 (2)°. The pyridinium cations are hydrogen bonded to the carboxyl-ate group by way of N-H⋯O links.
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