Displaying publications 21 - 40 of 49 in total

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  1. Micro-bending based optical band-pass filter and its application in S-band Thulium-doped fiber amplifier
    Emami SD, Rashid HA, Zarifi A, Zarei A, Soltanian MR, Yasin SZ, et al.
    Opt Express, 2012 Dec 31;20(28):29784-97.
    PMID: 23388806 DOI: 10.1364/OE.20.029784
    A new approach for filtering an optical band-pass in optical amplifier is proposed using a macro bending. The proposed filter leverages the bending loss of higher order modes at shorter wavelengths. At longer wavelengths, the filter increases fiber's bending loss as the fundamental mode 'tail' is leak out from the cladding. The combination of wavelength dependent loss at longer and shorter wavelength gives rise to the optical band-pass filter characteristic inside the fiber. The simulated spectral response of the filter is found to be in good agreement with the experimental results. Subsequently, the proposed optical band-pass filter is applied in Thulium-doped fiber amplifiers (TDFA) system for gain and noise figure enhancements. The filter functions to suppress both the amplified spontaneous emission (ASE) at 800 nm and 1800 nm wavelength regions and thus improves both gain and noise figure performances in S-band region. By bending of the gain medium, gain and noise figure of the TDFA are improved by about 2 dB and 0.5 dB respectively, within a wavelength region from 1440 and 1500 nm when the 1050 nm pump power is fixed at 250 mW.
  2. Biotechnological route for sustainable succinate production utilizing oil palm frond and kenaf as potential carbon sources
    Luthfi AAI, Manaf SFA, Illias RM, Harun S, Mohammad AW, Jahim JM
    Appl Microbiol Biotechnol, 2017 Apr;101(8):3055-3075.
    PMID: 28280869 DOI: 10.1007/s00253-017-8210-z
    Due to the world's dwindling energy supplies, greater thrust has been placed on the utilization of renewable resources for global succinate production. Exploration of such biotechnological route could be seen as an act of counterbalance to the continued fossil fuel dominance. Malaysia being a tropical country stands out among many other nations for its plenty of resources in the form of lignocellulosic biomass. To date, oil palm frond (OPF) contributes to the largest fraction of agricultural residues in Malaysia, while kenaf, a newly introduced fiber crop with relatively high growth rate, holds great potential for developing sustainable succinate production, apart from OPF. Utilization of non-food, inexhaustible, and low-cost derived biomass in the form of OPF and kenaf for bio-based succinate production remains largely untapped. Owing to the richness of carbohydrates in OPF and kenaf, bio-succinate commercialization using these sources appears as an attractive proposition for future sustainable developments. The aim of this paper was to review some research efforts in developing a biorefinery system based on OPF and kenaf as processing inputs. It presents the importance of the current progress in bio-succinate commercialization, in addition to describing the potential use of different succinate production hosts and various pretreatments-saccharifications under development for OPF and kenaf. Evaluations on the feasibility of OPF and kenaf as fermentation substrates are also discussed.
  3. Fulltext Telescopic synthesis of cellulose nanofibrils with a stable dispersion of Fe(0) nanoparticles for synergistic removal of 5-fluorouracil
    Sajab MS, Mohan D, Santanaraj J, Chia CH, Kaco H, Harun S, et al.
    Sci Rep, 2019 08 12;9(1):11703.
    PMID: 31406228 DOI: 10.1038/s41598-019-48274-2
    The recognition of cellulose nanofibrils (CNF) in the past years as a high prospect material has been prominent, but the impractical cellulose extraction method from biomass remained as a technological barrier for industrial practice. In this study, the telescopic approach on the fractionation of lignin and cellulose was performed by organosolv extraction and catalytic oxidation from oil palm empty fruit bunch fibers. The integration of these techniques managed to synthesize CNF in a short time. Aside from the size, the zeta potential of CNF was measured at -41.9 mV, which allow higher stability of the cellulose in water suspension. The stability of CNF facilitated a better dispersion of Fe(0) nanoparticles with the average diameter size of 52.3-73.24 nm through the formulation of CNF/Fe(0). The total uptake capacity of CNF towards 5-fluorouracil was calculated at 0.123 mg/g. While the synergistic reactions of adsorption-oxidation were significantly improved the removal efficacy three to four times greater even at a high concentration of 5-fluorouracil. Alternatively, the sludge generation after the oxidation reaction was completely managed by the encapsulation of Fe(0) nanoparticles in regenerated cellulose.
  4. Compatibility of utilising nitrogen-rich oil palm trunk sap for succinic acid fermentation by Actinobacillus succinogenes 130Z
    Bukhari NA, Loh SK, Nasrin AB, Luthfi AAI, Harun S, Abdul PM, et al.
    Bioresour Technol, 2019 Dec;293:122085.
    PMID: 31499328 DOI: 10.1016/j.biortech.2019.122085
    In this study, the potential of oil palm trunk (OPT) sap as a sole substrate for succinic acid (SA) production was evaluated using Actinobacillus succinogenes 130Z. After OPT sap was characterised, the effects of adding carbonate, yeast extract (YE) and minerals to this medium were investigated in an attempt to develop a low-cost fermentation medium. The OPT sap alone, gave comparable SA yield and productivity (0.54 g/g and 0.35 g/L/h) to those supplemented with YE (0.50 g/g and 0.36 g/L/h) and minerals (0.55 g/g and 0.40 g/L/h). The findings showed that OPT sap has sufficient amount of nutrients for SA biosynthesis by A. succinogenes 130Z and could potentially reduce cost without requiring expensive nutrients supplementation.
  5. Fulltext Potential Arabidopsis thaliana glucosinolate genes identified from the co-expression modules using graph clustering approach
    Harun S, Afiqah-Aleng N, Karim MB, Altaf Ul Amin M, Kanaya S, Mohamed-Hussein ZA
    PeerJ, 2021;9:e11876.
    PMID: 34430080 DOI: 10.7717/peerj.11876
    Background: Glucosinolates (GSLs) are plant secondary metabolites that contain nitrogen-containing compounds. They are important in the plant defense system and known to provide protection against cancer in humans. Currently, increasing the amount of data generated from various omics technologies serves as a hotspot for new gene discovery. However, sometimes sequence similarity searching approach is not sufficiently effective to find these genes; hence, we adapted a network clustering approach to search for potential GSLs genes from the Arabidopsis thaliana co-expression dataset.

    Methods: We used known GSL genes to construct a comprehensive GSL co-expression network. This network was analyzed with the DPClusOST algorithm using a density of 0.5. 0.6. 0.7, 0.8, and 0.9. Generating clusters were evaluated using Fisher's exact test to identify GSL gene co-expression clusters. A significance score (SScore) was calculated for each gene based on the generated p-value of Fisher's exact test. SScore was used to perform a receiver operating characteristic (ROC) study to classify possible GSL genes using the ROCR package. ROCR was used in determining the AUC that measured the suitable density value of the cluster for further analysis. Finally, pathway enrichment analysis was conducted using ClueGO to identify significant pathways associated with the GSL clusters.

    Results: The density value of 0.8 showed the highest area under the curve (AUC) leading to the selection of thirteen potential GSL genes from the top six significant clusters that include IMDH3, MVP1, T19K24.17, MRSA2, SIR, ASP4, MTO1, At1g21440, HMT3, At3g47420, PS1, SAL1, and At3g14220. A total of Four potential genes (MTO1, SIR, SAL1, and IMDH3) were identified from the pathway enrichment analysis on the significant clusters. These genes are directly related to GSL-associated pathways such as sulfur metabolism and valine, leucine, and isoleucine biosynthesis. This approach demonstrates the ability of the network clustering approach in identifying potential GSL genes which cannot be found from the standard similarity search.

  6. Fulltext Optical and Photoacoustic Properties of Laser-Ablated Silver Nanoparticles in a Carbon Dots Solution
    Sadrolhosseini AR, Krishnan G, Shafie S, Abdul Rashid S, Wadi Harun S
    Molecules, 2020 Dec 09;25(24).
    PMID: 33316885 DOI: 10.3390/molecules25245798
    This study used the carbon dots solution for the laser ablation technique to fabricate silver nanoparticles. The ablation time range was from 5 min to 20 min. Analytical methods, including Fourier transform infrared spectroscopy (FTIR), UV-visible spectroscopy, transmission electron microscopy, and Raman spectroscopy were used to categorize the prepared samples. The UV-visible and z-scan techniques provided optical parameters such as linear and nonlinear refractive indices in the range of 1.56759 to 1.81288 and 7.3769 × 10-10 cm2 W-1 to 9.5269 × 10-10 cm2 W-1 and the nonlinear susceptibility was measured in the range of 5.46 × 10-8 to 6.97 × 10-8 esu. The thermal effusivity of prepared samples, which were measured using the photoacoustic technique, were in the range of 0.0941 W s1/2 cm-2 K-1 to 0.8491 W s1/2 cm-2 K-1. The interaction of the prepared sample with fluoride was investigated using a Raman spectrometer. Consequently, the intensity of the Raman signal decreased with the increasing concentration of fluoride, and the detection limit is about 0.1 ppm.
  7. Homogeneous solid dispersion (HSD) system for rapid and stable production of succinic acid from lignocellulosic hydrolysate
    Luthfi AAI, Tan JP, Harun S, Manaf SFA, Jahim JM
    Bioprocess Biosyst Eng, 2019 Jan;42(1):117-130.
    PMID: 30259181 DOI: 10.1007/s00449-018-2019-8
    Continuous bio-production of succinic acid was reported in homogeneous solid dispersion (HSD) system utilizing porous coconut shell activated carbon (CSAC) as immobilization carrier. The aim of the present work was to implement the HSD system to increase the area of cell immobilization and the rate of succinic-acid production from the lignocellulosic medium. The ratio of the two enzymes (cellulase-to-hemicellulase) was initially optimized to break down the lignocellulose into its free monomers, wherein the best ratio was determined as 4:1. Succinic-acid production was evaluated in the HSD system by varying the substrate loading and dilution rate. The results showed that high productivities of succinic acid were obtained when 60 g/L glucose was fed over a dilution rates ranging from 0.03 to 0.4/h. The titer of succinic acid decreased gradually with higher dilution rate, whereas the residual substrate concentration increased with it. Critical dilution rate was determined to be 0.4/h at which the best productivity of succinic acid of 6.58 g/L h and its yield of 0.66 g/g were achieved using oil palm fronds (OPF) hydrolysate. This work lends evidence to the use of CSAC and lignocellulosic hydrolysate to further exploit the potential economies of scale.
  8. Fulltext PCOSBase: a manually curated database of polycystic ovarian syndrome
    Afiqah-Aleng N, Harun S, A-Rahman MRA, Nor Muhammad NA, Mohamed-Hussein ZA
    Database (Oxford), 2017 Jan 01;2017.
    PMID: 31725861 DOI: 10.1093/database/bax098
    Polycystic ovarian syndrome (PCOS) is one of the main causes of infertility and affects 5-20% women of reproductive age. Despite the increased prevalence of PCOS, the mechanisms involved in its pathogenesis and pathophysiology remains unclear. The expansion of omics on studying the mechanisms of PCOS has lead into vast amounts of proteins related to PCOS resulting to a challenge in collating and depositing this deluge of data into one place. A knowledge-based repository named as PCOSBase was developed to systematically store all proteins related to PCOS. These proteins were compiled from various online databases and published expression studies. Rigorous criteria were developed to identify those that were highly related to PCOS. They were manually curated and analysed to provide additional information on gene ontologies, pathways, domains, tissue localizations and diseases that associate with PCOS. Other proteins that might interact with PCOS-related proteins identified from this study were also included. Currently, 8185 PCOS-related proteins were identified and assigned to 13 237 gene ontology vocabulary, 1004 pathways, 7936 domains, 29 disease classes, 1928 diseases, 91 tissues and 320 472 interactions. All publications related to PCOS are also indexed in PCOSBase. Data entries are searchable in the main page, search, browse and datasets tabs. Protein advanced search is provided to search for specific proteins. To date, PCOSBase has the largest collection of PCOS-related proteins. PCOSBase aims to become a self-contained database that can be used to further understand the PCOS pathogenesis and towards the identification of potential PCOS biomarkers. Database URL: http://pcosbase.org.
  9. Fulltext SuCComBase: a manually curated repository of plant sulfur-containing compounds
    Harun S, Abdullah-Zawawi MR, A-Rahman MRA, Muhammad NAN, Mohamed-Hussein ZA
    Database (Oxford), 2019 01 01;2019.
    PMID: 30793170 DOI: 10.1093/database/baz021
    Plants produce a wide range of secondary metabolites that play important roles in plant defense and immunity, their interaction with the environment and symbiotic associations. Sulfur-containing compounds (SCCs) are a group of important secondary metabolites produced in members of the Brassicales order. SCCs constitute various groups of phytochemicals, but not much is known about them. Findings from previous studies on SCCs were scattered in published literatures, hence SuCComBase was developed to store all molecular information related to the biosynthesis of SCCs. Information that includes genes, proteins and compounds that are involved in the SCC biosynthetic pathway was manually identified from databases and published scientific literatures. Sets of co-expression data was analyzed to search for other possible (previously unknown) genes that might be involved in the biosynthesis of SCC. These genes were named as potential SCC-related encoding genes. A total of 147 known and 92 putative Arabidopsis thaliana SCC-related genes from literatures were used to identify other potential SCC-related encoding genes. We identified 778 potential SCC-related encoding genes, 4026 homologs to the SCC-related encoding genes and 116 SCCs as shown on SuCComBase homepage. Data entries are searchable from the Main page, Search, Browse and Datasets tabs. Users can easily download all data stored in SuCComBase. All publications related to SCCs are also indexed in SuCComBase, which is currently the first and only database dedicated to plant SCCs. SuCComBase aims to become a manually curated and au fait knowledge-based repository for plant SCCs.
  10. Fulltext Comparative genome-wide analysis of WRKY, MADS-box and MYB transcription factor families in Arabidopsis and rice
    Abdullah-Zawawi MR, Ahmad-Nizammuddin NF, Govender N, Harun S, Mohd-Assaad N, Mohamed-Hussein ZA
    Sci Rep, 2021 10 04;11(1):19678.
    PMID: 34608238 DOI: 10.1038/s41598-021-99206-y
    Transcription factors (TFs) form the major class of regulatory genes and play key roles in multiple plant stress responses. In most eukaryotic plants, transcription factor (TF) families (WRKY, MADS-box and MYB) activate unique cellular-level abiotic and biotic stress-responsive strategies, which are considered as key determinants for defense and developmental processes. Arabidopsis and rice are two important representative model systems for dicot and monocot plants, respectively. A comprehensive comparative study on 101 OsWRKY, 34 OsMADS box and 122 OsMYB genes (rice genome) and, 71 AtWRKY, 66 AtMADS box and 144 AtMYB genes (Arabidopsis genome) showed various relationships among TFs across species. The phylogenetic analysis clustered WRKY, MADS-box and MYB TF family members into 10, 7 and 14 clades, respectively. All clades in WRKY and MYB TF families and almost half of the total number of clades in the MADS-box TF family are shared between both species. Chromosomal and gene structure analysis showed that the Arabidopsis-rice orthologous TF gene pairs were unevenly localized within their chromosomes whilst the distribution of exon-intron gene structure and motif conservation indicated plausible functional similarity in both species. The abiotic and biotic stress-responsive cis-regulatory element type and distribution patterns in the promoter regions of Arabidopsis and rice WRKY, MADS-box and MYB orthologous gene pairs provide better knowledge on their role as conserved regulators in both species. Co-expression network analysis showed the correlation between WRKY, MADs-box and MYB genes in each independent rice and Arabidopsis network indicating their role in stress responsiveness and developmental processes.
  11. Fulltext Evaluating the Stability of PLA-Lignin Filament Produced by Bench-Top Extruder for Sustainable 3D Printing
    Zaidi SAS, Kwan CE, Mohan D, Harun S, Luthfi AAI, Sajab MS
    Materials (Basel), 2023 Feb 22;16(5).
    PMID: 36902909 DOI: 10.3390/ma16051793
    As additive manufacturing continues to evolve, there is ongoing discussion about ways to improve the layer-by-layer printing process and increase the mechanical strength of printed objects compared to those produced by traditional techniques such as injection molding. To achieve this, researchers are exploring ways of enhancing the interaction between the matrix and filler by introducing lignin in the 3D printing filament processing. In this work, research has been conducted on using biodegradable fillers of organosolv lignin, as a reinforcement for the filament layers in order to enhance interlayer adhesion by using a bench-top filament extruder. Briefly, it was found that organosolv lignin fillers have the potential to improve the properties of polylactic acid (PLA) filament for fused deposition modeling (FDM) 3D printing. By incorporating different formulations of lignin with PLA, it was found that using 3 to 5% lignin in the filament leads to an improvement in the Young's modulus and interlayer adhesion in 3D printing. However, an increment of up to 10% also results in a decrease in the composite tensile strength due to the lack of bonding between the lignin and PLA and the limited mixing capability of the small extruder.
  12. Enterprise resource planning implementation within science and technology park (STP) organisations: an avenue for future research. A systematic review
    Harun S, Dorasamy M, Bin Ahmad AA, Yap CS, Harguem S
    F1000Res, 2021;10:1148.
    PMID: 37599674 DOI: 10.12688/f1000research.73347.3
    Background: Enterprise resource planning (ERP) is critical to enhancing the ability to control commercial activities and results in a competitive advantage when combined with an organisation's existing competitive advantages. However, our practise review reveals that end users resist ERP implementation because the resulting changes will alter the current status quo. The implementation of an ERP system in an organisation is complex as it affects multiple areas of the business. Resistance to change is cited as a factor of ERP failure. Methods: In this study, we conducted a systematic literature review using Transfield's five stages and established a conceptual framework for ERP system implementation in science and technology parks (STPs). Articles collected from Emerald, Science Direct, ProQuest and Scopus databases between 1 st June 2021 and 15 th June 2021. Two authors were assigned to check the suitability of the articles in order to avoid risk of bias. Articles were analysed based on components of a research paper and the data was tabulated using MS Excel. Results: Only eight papers (0.011% of all the papers) appeared when we searched for papers related to ERP with a focus on post ERP Implementation, end-user behaviours, organisational performance, and the accelerated SAP (system application and product) methodology. We found that there are hardly any articles on ERP post implementations in STP context particularly based on the evaluation part of accelerated SAP.   Conclusions: Results indicate the lack of studies in this field, particularly those addressing issues related to STP. This study attempted to broaden the understanding of the ERP's effectiveness, particularly in terms of an organisation's operational performance.
  13. Healthcare-associated infections among neonates and children in Pakistan: findings and the implications from a point prevalence survey
    Mustafa ZU, Khan AH, Salman M, Harun SN, Meyer JC, Godman B, et al.
    J Hosp Infect, 2023 Nov;141:142-151.
    PMID: 37774930 DOI: 10.1016/j.jhin.2023.09.011
    BACKGROUND: Healthcare-associated infections (HAIs) increase morbidity, mortality and costs. The overall prevalence of HAIs is greater in low- and middle-income countries due to poor resources and infrastructure, with the incidence of HAIs greater among neonates and children. There is a need to understand the current situation in Pakistan including key drivers to improve future care.

    METHODS: Point prevalence survey (PPS) of HAIs in the children's wards of 19 public sector secondary- and tertiary-care hospitals of Pakistan and associated key drivers.

    RESULTS: A total of 1147 children were included in the PPS. 35.7% were neonates with 32.8% aged >1-5 years. 35.2% were admitted to the intensive care units (ICUs). Peripheral, central venous and urinary catheters were present in 48%, 2.9% and 5.6% of the patients, respectively. A total of 161 HAIs from various pathogens were observed in 153 cases, giving a prevalence of 13.3%. The majority of HAIs were caused by Staphylococcus aureus (31.7%) followed by Klebsiella pneumoniae (22.9%) and Escherichia coli (17.4%). Bloodstream infections were identified in 42 cases followed by lower-respiratory-tract infections in 35. Increased length of hospital stays and being admitted to the ICU, 'rapidly fatal' patients under the McCabe and Jackson criteria, central and peripheral catheterization, and invasive mechanical ventilation were, associated with higher HAIs (P<0.001). 99.7% of HAI patients fully recovered and were discharged from the hospital.

    CONCLUSION: There is a high prevalence of HAIs among neonates and children admitted to health facilities in Pakistan. Infection prevention and control measures should be implemented to help prevent future HAIs.

  14. Fulltext Synchronous online learning during movement control order in higher education institutions: a systematic review
    Lee YW, Dorasamy M, Bin Ahmad AA, Jambulingam M, Yeap PF, Harun S
    F1000Res, 2021;10:1056.
    PMID: 34950456 DOI: 10.12688/f1000research.73342.2
    Background: Higher education institutions (HEI) are not spared from the coronavirus disease 2019 (COVID-19) pandemic. The closure of campuses because of the movement control order (MCO) to mitigate the spread of the COVID-19 has forced HEIs to adopt online learning, especially synchronous online learning (SOL). Although teaching and learning can be continued via SOL, retaining students' interest and sustaining their engagement have not been sufficiently explored. This study presents a systematic review of the research pertaining to SOL associated with students' interest and engagement in HEIs during the MCO environment. Methods: Five major online databases, i.e., EBSCOhost, Science Direct, Emerald, Scopus and Springer were searched to collect relevant papers published between 1st January 2010 to 15th June 2021 including conference proceedings, peer-reviewed papers and dissertations. Papers written in the English language, based in full-fledged universities, and with these five keywords: (i) synchronous online learning, (ii) engagement, (iii) interest, (iv) MCO/Covid-19 and (v) HEI, were included. Papers focussing on synchronous and asynchronous online learning in schools and colleges were excluded. Each paper was reviewed by two reviewers in order to confirm the eligibility based on the inclusion and exclusion criteria. Results: We found 31 papers of which six papers were related to SOL, engagement and interest in HEIs in the MCO environment. Our review presents three major findings: (i) limited research has been conducted on SOL associated with students' engagement and interest, (ii) studies related to the context of HEIs in the MCO environment are limited, and (iii) the understanding of the new phenomena through qualitative research is insufficient. We highlight the SOL alignment with students' engagement, interest, style preference, learner interaction effectiveness, behavior and academic performance. Conclusions: We believe that the findings of this study are timely and require attention from the research community.
  15. Fulltext Prevalence of Stroke-Associated Pneumonia and Its Predictors Among Hyperglycaemia Patients During Acute Ischemic Stroke
    Elhefnawy M, Nazifah Sidek N, Maisharah Sheikh Ghadzi S, Ibrahim B, Looi I, Abdul Aziz Z, et al.
    Cureus, 2024 Jan;16(1):e52574.
    PMID: 38371076 DOI: 10.7759/cureus.52574
    BACKGROUND: Hyperglycaemia (HG) during an acute ischemic stroke (AIS) is not only associated with unfavourable functional outcomes but also associated with stroke-associated pneumonia (SAP). This study aimed to determine the prevalence of SAP among Malaysian patients with AIS and the predictors of SAP among patients with HG during AIS.

    METHODS: This is a retrospective cross-sectional study that included patients with AIS admitted to Hospital Sultanah Nur Zahirah, Malaysia from 2017 to 2020. SAP was defined as infection with pneumonia during the first seven days after IS. HG was defined as a blood glucose level > 7.8 mmol/L within 72 h after admission. Patients with SAP were divided into two groups according to HG status. Multivariate logistic regression analysis was performed using SPSS software, version 22 (IBM Corp., Armonk, NY) to identify SAP predictors among patients with HG. Kaplan-Meier log-rank test was used to compare the survival rate from unfavourable functional outcomes between hyperglycaemic patients with and without SAP.

    RESULTS: Among 412 patients with AIS, 69 (16.74%) had SAP. The prevalence of SAP among patients with HG and normoglycemia during AIS was 20.98%, and 10.65%, respectively. Age above 60 years, leucocytosis, and National Institute of Health Stroke Scale (NIHSS) > 14 on admission were independent predictors of SAP with aOR of 2.08 (95% CI;1.01-4.30), 2.83 (95% CI; 1.41-5.67), and 3.67 (95% CI; 1.53-8.80), respectively. No significant difference in unfavourable functional outcomes survival was found among patients with and without SAP (p = 0.653).

    CONCLUSION: This study demonstrated the prevalence of SAP was higher among patients with HG compared to normoglycemia during AIS. The patient being old, leucocytosis and severe stroke upon admission predict the occurrence of SAP among patients with HG during AIS.

  16. Fulltext A Stable Dual-wavelength Thulium-doped Fiber Laser at 1.9 μm Using Photonic Crystal Fiber
    Soltanian MR, Ahmad H, Khodaie A, Amiri IS, Ismail MF, Harun SW
    Sci Rep, 2015 Oct 12;5:14537.
    PMID: 26455713 DOI: 10.1038/srep14537
    A stable dual-wavelength thulium-doped fiber laser operating at 1.9 μm using a short length of photonic crystal fiber (PCF) has been proposed and demonstrated. The photonics crystal fiber was 10 cm in length and effectively acted as a Mach-Zehnder interferometry element with a free spectral range of 0.2 nm. This dual-wavelength thulium-doped fiber laser operated steadily at room temperature with a 45 dB optical signal-to-noise-ratio.
  17. Cross Talk between MicroRNAs and Dengue Virus
    Macha NO, Komarasamy TV, Harun S, Adnan NAA, Hassan SS, Balasubramaniam VRMT
    Am J Trop Med Hyg, 2024 May 01;110(5):856-867.
    PMID: 38579704 DOI: 10.4269/ajtmh.23-0546
    Dengue fever (DF) is an endemic infectious tropical disease and is rapidly becoming a global problem. Dengue fever is caused by one of the four dengue virus (DENV) serotypes and is spread by the female Aedes mosquito. Clinical manifestations of DF may range from asymptomatic to life-threatening severe illness with conditions of hemorrhagic fever and shock. Early and precise diagnosis is vital to avoid mortality from DF. A different approach is required to combat DF because of the challenges with the vaccines currently available, which are nonspecific; each is capable of causing cross-reaction and disease-enhancing antibody responses against the residual serotypes. MicroRNAs (miRNAs) are known to be implicated in DENV infection and are postulated to be involved in most of the host responses. Thus, they might be a suitable target for new strategies against the disease. The involvement of miRNAs in cellular activities and pathways during viral infections has been explored under numerous conditions. Interestingly, miRNAs have also been shown to be involved in viral replication. In this review, we summarize the role of known miRNAs, specifically the role of miRNA Let-7c (miR-Let-7c), miR-133a, miR-30e, and miR-146a, in the regulation of DENV replication and their possible effects on the initial immune reaction.
  18. Exploring gene regulation and biological processes in insects: Insights from omics data using gene regulatory network models
    Chee FT, Harun S, Mohd Daud K, Sulaiman S, Nor Muhammad NA
    Prog Biophys Mol Biol, 2024 Apr 09;189:1-12.
    PMID: 38604435 DOI: 10.1016/j.pbiomolbio.2024.04.002
    Gene regulatory network (GRN) comprises complicated yet intertwined gene-regulator relationships. Understanding the GRN dynamics will unravel the complexity behind the observed gene expressions. Insect gene regulation is often complicated due to their complex life cycles and diverse ecological adaptations. The main interest of this review is to have an update on the current mathematical modelling methods of GRNs to explain insect science. Several popular GRN architecture models are discussed, together with examples of applications in insect science. In the last part of this review, each model is compared from different aspects, including network scalability, computation complexity, robustness to noise and biological relevancy.
  19. Fulltext Multi-Omics Approaches and Resources for Systems-Level Gene Function Prediction in the Plant Kingdom
    Abdullah-Zawawi MR, Govender N, Harun S, Muhammad NAN, Zainal Z, Mohamed-Hussein ZA
    Plants (Basel), 2022 Oct 05;11(19).
    PMID: 36235479 DOI: 10.3390/plants11192614
    In higher plants, the complexity of a system and the components within and among species are rapidly dissected by omics technologies. Multi-omics datasets are integrated to infer and enable a comprehensive understanding of the life processes of organisms of interest. Further, growing open-source datasets coupled with the emergence of high-performance computing and development of computational tools for biological sciences have assisted in silico functional prediction of unknown genes, proteins and metabolites, otherwise known as uncharacterized. The systems biology approach includes data collection and filtration, system modelling, experimentation and the establishment of new hypotheses for experimental validation. Informatics technologies add meaningful sense to the output generated by complex bioinformatics algorithms, which are now freely available in a user-friendly graphical user interface. These resources accentuate gene function prediction at a relatively minimal cost and effort. Herein, we present a comprehensive view of relevant approaches available for system-level gene function prediction in the plant kingdom. Together, the most recent applications and sought-after principles for gene mining are discussed to benefit the plant research community. A realistic tabulation of plant genomic resources is included for a less laborious and accurate candidate gene discovery in basic plant research and improvement strategies.
  20. Mode-locked thulium-bismuth codoped fiber laser using graphene saturable absorber in ring cavity
    Zen DI, Saidin N, Damanhuri SS, Harun SW, Ahmad H, Ismail MA, et al.
    Appl Opt, 2013 Feb 20;52(6):1226-9.
    PMID: 23434993 DOI: 10.1364/AO.52.001226
    We demonstrate mode locking of a thulium-bismuth codoped fiber laser (TBFL) operating at 1901.6 nm, using a graphene-based saturable absorber (SA). In this work, a single layer graphene is mechanically exfoliated using the scotch tape method and directly transferred onto the surface of a fiber pigtail to fabricate the SA. The obtained Raman spectrum characteristic indicates that the graphene on the core surface has a single layer. At 1552 nm pump power of 869 mW, the mode-locked TBFL self starts to generate an optical pulse train with a repetition rate of 16.7 MHz and pulse width of 0.37 ps. This is a simple, low-cost, stable, and convenient laser oscillator for applications where eye-safe and low-photon-energy light sources are required, such as sensing and biomedical diagnostics.
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