Displaying publications 1 - 20 of 22 in total

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  1. Health-related quality of life after 6 months post-injury on severe traumatic brain injury: A cohort study in two Malaysian hospitals
    Ludin SM, Rashid NA
    Enferm Clin, 2019 09;29 Suppl 2:674-680.
    PMID: 31311746 DOI: 10.1016/j.enfcli.2019.04.103
    OBJECTIVE: Severe traumatic brain injury (TBI) survivors show physical and functional improvement but remain with the cognitive and psycho-social problem through our recovery. This study aims to measure the health-related quality of life of TBI survivors within 6 months post-injury.

    METHOD: A cohort study was conducted where 33 severe TBI survivors recruited at two tertiary hospitals. The health-related quality of life was measured using the Quality of Life after Brain Injury (QOLIBRI) tool.

    RESULTS: Participants mean age was 31.79 years old. The impaired range of health-related quality of life on 6 months post-injury seen, but an improvement occurs within 3-6 months post-injury.

    CONCLUSIONS: Age and ventilation duration showed a moderate negative correlation in all domains and length of hospital stay showed a moderate negative correlation to social, daily life and self-domains. Nevertheless, small sample size and time constraint were the limitations of this study.

  2. Fast decision tree-based method to index large DNA-protein sequence databases using hybrid distributed-shared memory programming model
    Jaber KM, Abdullah R, Rashid NA
    Int J Bioinform Res Appl, 2014;10(3):321-40.
    PMID: 24794073 DOI: 10.1504/IJBRA.2014.060765
    In recent times, the size of biological databases has increased significantly, with the continuous growth in the number of users and rate of queries; such that some databases have reached the terabyte size. There is therefore, the increasing need to access databases at the fastest rates possible. In this paper, the decision tree indexing model (PDTIM) was parallelised, using a hybrid of distributed and shared memory on resident database; with horizontal and vertical growth through Message Passing Interface (MPI) and POSIX Thread (PThread), to accelerate the index building time. The PDTIM was implemented using 1, 2, 4 and 5 processors on 1, 2, 3 and 4 threads respectively. The results show that the hybrid technique improved the speedup, compared to a sequential version. It could be concluded from results that the proposed PDTIM is appropriate for large data sets, in terms of index building time.
  3. Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure
    Al-Khatib RM, Rashid NA, Abdullah R
    J Biomol Struct Dyn, 2011 Aug;29(1):1-26.
    PMID: 21696223
    The secondary structure of RNA pseudoknots has been extensively inferred and scrutinized by computational approaches. Experimental methods for determining RNA structure are time consuming and tedious; therefore, predictive computational approaches are required. Predicting the most accurate and energy-stable pseudoknot RNA secondary structure has been proven to be an NP-hard problem. In this paper, a new RNA folding approach, termed MSeeker, is presented; it includes KnotSeeker (a heuristic method) and Mfold (a thermodynamic algorithm). The global optimization of this thermodynamic heuristic approach was further enhanced by using a case-based reasoning technique as a local optimization method. MSeeker is a proposed algorithm for predicting RNA pseudoknot structure from individual sequences, especially long ones. This research demonstrates that MSeeker improves the sensitivity and specificity of existing RNA pseudoknot structure predictions. The performance and structural results from this proposed method were evaluated against seven other state-of-the-art pseudoknot prediction methods. The MSeeker method had better sensitivity than the DotKnot, FlexStem, HotKnots, pknotsRG, ILM, NUPACK and pknotsRE methods, with 79% of the predicted pseudoknot base-pairs being correct.
  4. Effects of chemical interesterification on the physicochemical, microstructural and thermal properties of palm stearin, palm kernel oil and soybean oil blends
    Fauzi SH, Rashid NA, Omar Z
    Food Chem, 2013 Apr 15;137(1-4):8-17.
    PMID: 23199984 DOI: 10.1016/j.foodchem.2012.09.086
    Blends of palm stearin (PS), palm kernel oil (PKO) and soybean oil (SBO) at certain proportions were formulated using a mixture design based on simplex-lattice (Design Expert 8.0.4 Stat-Ease Inc., Minneapolis, 2010). All the 10 oil blends were subjected to chemical interesterification (CIE) using sodium methoxide as the catalyst. The solid fat content (SFC), triacylglycerol (TAG) composition, thermal properties (DSC), polymorphism and microstructural properties were studied. Palm-based trans-free table margarine containing ternary mixture of PS/PKO/SBO [49/20/31 (w/w)], was optimally formulated through analysis of multiple isosolid diagrams and was found to have quite similar SMP and SFC profile as compared to the commercial table margarine. This study has shown chemical interesterification are effective in modifying the physicochemical properties of palm stearin, palm kernel oil, soybean oil and their mixtures.
  5. Fulltext Predicting generalized anxiety disorder among women using Shapley value
    Jothi N, Husain W, Rashid NA
    J Infect Public Health, 2021 Jan;14(1):103-108.
    PMID: 32273237 DOI: 10.1016/j.jiph.2020.02.042
    Mental illness is a set of health problems that affect the way individuals perceive themselves, relate to others, and interact with the world around them. Due to the myriad of underlying causes and subsequent effects of mental illness, these conditions often trigger fear and misunderstanding among the general population. Common mental illnesses such as depression and anxiety disorders often affect an individual's thoughts, feelings, abilities, and behaviours. Anxiety disorder is characterized by an irrational fear of certain things or events. It is often attributed as the feeling of worry about anticipated events and fear in response to current events. This work has identified several related research efforts on the general well-being and psychological distress using data mining. However, there is inadequate research done using a similar method on specific mental health issues, especially related to generalized anxiety disorder (GAD). In view of this gap, this study focuses on implementing a novel feature selection and data mining classifier system. Under the proposed method, Shapley value will be implemented as the feature selection of the data mining classifier on the mental health data. The approach is used to predict GAD among women. The methodology for this research is adapted from the process of Knowledge Discovery in Databases (KDD). This methodology consists of 5 main phases; namely data acquisition, data pre-processing, feature selection, classification prediction, and evaluation. Using this enhanced prediction algorithm, any women can get help if they are perceived to be suffering from GAD. By designing an effective way of identifying individuals who may be suffering from mental illnesses, we hope that our work would improve the awareness surrounding mental health issues especially among women and enable them to undertake autonomous decision in seeking mental health services.
  6. Fulltext Exploratory analysis of traditional risk factors of ischemic heart disease (IHD) among predominantly Malay Malaysian women
    Rashid NA, Nawi AM, Khadijah S
    BMC Public Health, 2019 Jun 13;19(Suppl 4):545.
    PMID: 31196022 DOI: 10.1186/s12889-019-6855-5
    BACKGROUND: The risk factors of ischemic heart disease (IHD) specific for women are less well studied. However, knowing the risk factors of IHD for women will empower women themselves to be better informed and thus can help them in decision making concerning their health condition. The objective of this study is to explore the commonly studied risk factors of ischemic heart disease (IHD) among a group of Malaysian women.

    METHODS: A case control study was conducted among 142 newly diagnosed IHD women patients registered in government hospitals in Terengganu, Malaysia and their 1:1 frequency matched population controls. Data on sociodemographic and socioeconomic profile, co-morbidities, lifestyle factors related to physical activities, dietary fat intake, stress, passive smoking history, anthropometric measurements and biochemical markers were obtained.

    RESULTS: Middle aged women were recruited with women diagnosed with diabetes (aOR = 1.92, 95% CI: 1.11-3.31), having low HDL-C (aOR = 3.30, 95% CI: 1.28-8.27), those with positive family history of IHD (aOR = 1.92, 95% CI:1.13-3.26) and passive smokers (aOR = 2.99, 95% CI:1.81-4.94) were at higher odds of IHD.

    CONCLUSIONS: The findings are useful for public health interventions and policy making focusing on specific women population.

  7. A comparative taxonomy of parallel algorithms for RNA secondary structure prediction
    Al-Khatib RM, Abdullah R, Rashid NA
    Evol Bioinform Online, 2010 Apr 09;6:27-45.
    PMID: 20458364
    RNA molecules have been discovered playing crucial roles in numerous biological and medical procedures and processes. RNA structures determination have become a major problem in the biology context. Recently, computer scientists have empowered the biologists with RNA secondary structures that ease an understanding of the RNA functions and roles. Detecting RNA secondary structure is an NP-hard problem, especially in pseudoknotted RNA structures. The detection process is also time-consuming; as a result, an alternative approach such as using parallel architectures is a desirable option. The main goal in this paper is to do an intensive investigation of parallel methods used in the literature to solve the demanding issues, related to the RNA secondary structure prediction methods. Then, we introduce a new taxonomy for the parallel RNA folding methods. Based on this proposed taxonomy, a systematic and scientific comparison is performed among these existing methods.
  8. Fulltext Genome sequence of Aureobasidium pullulans AY4, an emerging opportunistic fungal pathogen with diverse biotechnological potential
    Chan GF, Bamadhaj HM, Gan HM, Rashid NA
    Eukaryotic Cell, 2012 Nov;11(11):1419-20.
    PMID: 23104371 DOI: 10.1128/EC.00245-12
    Aureobasidium pullulans AY4 is an opportunistic pathogen that was isolated from the skin of an immunocompromised patient. We present here the draft genome of strain AY4, which reveals an abundance of genes relevant to bioindustrial applications, including biocontrol and biodegradation. Putative genes responsible for the pathogenicity of strain AY4 were also identified.
  9. Fulltext Genome sequence of Pichia kudriavzevii M12, a potential producer of bioethanol and phytase
    Chan GF, Gan HM, Ling HL, Rashid NA
    Eukaryotic Cell, 2012 Oct;11(10):1300-1.
    PMID: 23027839 DOI: 10.1128/EC.00229-12
    A draft genome sequence of Pichia kudriavzevii M12 is presented here. The genome reveals the presence of genes encoding enzymes involved in xylose utilization and the pentose phosphate pathway for bioethanol production. Strain M12 is also a potential producer of phytases, enzymes useful in food processing and agriculture.
  10. Functional Outcomes 6 Months After Severe Traumatic Brain Injury Following Admission Into Intensive Care Unit: A Cohort Study in Two Tertiary Hospitals
    Ludin SM, Rashid NA, Awang MS, Nor MBM
    Clin Nurs Res, 2019 09;28(7):830-851.
    PMID: 29618232 DOI: 10.1177/1054773818767551
    Severe traumatic brain injury (TBI) survivors show physical and functional improvements but continue to have cognitive and psychosocial problems throughout recovery. However, the functional outcome of severe TBI in Malaysia is unknown. The objective of this study is to measure the functional outcomes of severe TBI within 6 months post-injury. A cohort study was done on 33 severe TBI survivors. The Glasgow Outcome Scale-Extended (GOSE) was used in this study. The mean age of the participants was 31.79 years (range: 16-73 years). The logistic regression model was statistically significant, χ²(5, N = 33) = 29.09, p < .001. The length of stay (LOS) in incentive care unit (p = .049, odds ratio = 6.062) and duration on ventilator (p = .048, odds ratio = 0.083) were good predictors of the functional outcomes. Future research should focus on larger sample size of severe TBI in Malaysia.
  11. Genome sequence of Enterococcus sp. strain C1, an azo dye decolorizer
    Chan GF, Gan HM, Rashid NA
    J Bacteriol, 2012 Oct;194(20):5716-7.
    PMID: 23012290
    Enterococcus sp. strain C1 is a facultative anaerobe which was coisolated with Citrobacter sp. strain A1 from a sewage oxidation pond. Strain C1 could degrade azo dyes very efficiently via azo reduction and desulfonation in a microaerophilic environment. Here the draft genome sequence of Enterococcus sp. C1 is reported.
  12. Fulltext Genome sequence of Citrobacter sp. strain A1, a dye-degrading bacterium
    Chan GF, Gan HM, Rashid NA
    J Bacteriol, 2012 Oct;194(19):5485-6.
    PMID: 22965102 DOI: 10.1128/JB.01285-12
    Citrobacter sp. strain A1, isolated from a sewage oxidation pond, is a facultative aerobe and mesophilic dye-degrading bacterium. This organism degrades azo dyes efficiently via azo reduction and desulfonation, followed by the successive biotransformation of dye intermediates under an aerobic environment. Here we report the draft genome sequence of Citrobacter sp. A1.
  13. Differential toxicity and teratogenic effects of the hot water and cold water extracts of Lignosusrhinocerus (Cooke) Ryvarden sclerotium on zebrafish (Danio rerio) embryos
    Abd Rashid NA, Lau BF, Kue CS
    J Ethnopharmacol, 2022 Mar 01;285:114787.
    PMID: 34756971 DOI: 10.1016/j.jep.2021.114787
    ETHNOPHARMACOLOGICAL RELEVANCE: The sclerotium of Lignosusrhinocerus (Cooke) Ryvarden is highly valued for its purported medicinal properties. The decoction and macerated materials prepared from the sclerotium are used for treating cancer and other ailments based on extensive traditional knowledge. Scientific evidence from in vitro cytototoxicity, anti-inflammatory and immunomodulatory analyses showed the effectiveness of sclerotial water extracts but toxicity assessment of such preparations has not been reported.

    AIM OF THE STUDY: This study aimed to compare the differential toxicity and teratogenicity (if any) of the hot water (HW) and cold water (CW) extracts of both wild and cultivated sclerotium on zebrafish (Danio rerio) embryos.

    MATERIALS AND METHODS: Zebrafish embryos were treated with varying concentrations of the sclerotial HW and CW extracts (0.3-500 μg/mL) for 72 h until hatching. The hatching, mortality and heartbeat rate of the embryos as well as the potential teratogenic effect of the extracts were assessed in embryos post-treatment with the extracts.

    RESULTS: While the sclerotial HW extracts were nontoxic (LC50 > 500 μg/mL), the sclerotial CW extracts delayed the hatching of the embryos up to 48 h and showed slight toxicity with LC50 values of 398.4 μg/mL and 428.3 μg/mL for the cultivated and wild sclerotium, respectively. The sclerotial CW extracts also induced minor tachycardia in zebrafish larvae. Phenotypic assessment revealed that, while yolk sac edema was observed at high concentrations (300 and 500 μg/mL) of all extracts, curved trunk and bent tail were only observed in the embryos treated with CW extracts of wild sclerotium (300 and 500 μg/mL) but not for CW extracts of cultivated sclerotium at similar concentrations.

    CONCLUSION: The sclerotial water extracts of L.rhinocerus prepared using different methods have varying degree of toxicity and teratogenicity in zebrafish embryos with the sclerotial CW extracts showed higher toxicity than the HW extracts.

  14. Simultaneous acid red 27 decolourisation and bioelectricity generation in a (H-type) microbial fuel cell configuration using NAR-2
    Kardi SN, Ibrahim N, Rashid NA, Darzi GN
    Environ Sci Pollut Res Int, 2016 Feb;23(4):3358-64.
    PMID: 26490910 DOI: 10.1007/s11356-015-5538-8
    Microbial fuel cells (MFCs) represent one of the most attractive and eco-friendly technologies that convert chemical bond energy derived from organic matter into electrical power by microbial catabolic activity. This paper presents the use of a H-type MFC involving a novel NAR-2 bacterial consortium consisting of Citrobacter sp. A1, Enterobacter sp. L17 and Enterococcus sp. C1 to produce electricity whilst simultaneously decolourising acid red 27 (AR27) as a model dye, which is also known as amaranth. In this setup, the dye AR27 is mixed with modified P5 medium (2.5 g/L glucose and 5.0 g/L nutrient broth) in the anode compartment, whilst phosphate buffer solution (PBS) pH 7 serves as a catholyte in the cathode compartment. After several electrochemical analyses, the open circuit voltage (OCV) for 0.3 g/L AR27 with 24-h retention time at 30 °C was recorded as 0.950 V, whereas (93%) decolourisation was achieved in 220-min operation. The maximum power density was reached after 48 h of operation with an external load of 300 Ω. Scanning electron microscopy (SEM) analysis revealed the surface morphology of the anode and the bacterial adhesion onto the electrode surface. The results of this study indicate that the decolourisation of AR27 dye and electrical power generation was successfully achieved in a MFC operated by a bacterial consortium. The consortium of bacteria was able to utilise AR27 in a short retention time as an electron acceptor and to shuttle the electrons to the anode surface for bioelectricity generation.
  15. Emergence of Aureobasidium pullulans as human fungal pathogen and molecular assay for future medical diagnosis
    Chan GF, Puad MS, Chin CF, Rashid NA
    Folia Microbiol (Praha), 2011 Sep;56(5):459-67.
    PMID: 21909832 DOI: 10.1007/s12223-011-0070-9
    Despite the great importance of Aureobasidium pullulans in biotechnology, the fungus had emerged as an opportunistic human pathogen, especially among immunocompromised patients. Clinical detection of this rare human fungal pathogen presently relies on morphology diagnosis which may be misleading. Thus, a sensitive and accurate quantitative molecular assay for A. pullulans remains lacking. In this study, we presented the microscopy observations of A. pullulans that reveals the phenotypic plasticity of the fungus. A. pullulans-specific primers and molecular beacon probes were designed based on the fungal 18S ribosomal RNA (rRNA) gene. Comparison of two probes with varied quencher chemistry, namely BHQ-1 and Tamra, revealed high amplification efficiency of 104% and 108%, respectively. The optimized quantitative real-time PCR (qPCR) assays could detect and quantify up to 1 pg concentration of A. pullulans DNA. Both assays displayed satisfactory performance parameters at fast thermal cycling mode. The molecular assay has great potential as a molecular diagnosis tool for early detection of fungal infection caused by A. pullulans, which merits future study in clinical diagnosis.
  16. Chest tube injury to left ventricle: complication or negligence?
    Haron H, Rashid NA, Dimon MZ, Azmi MH, Sumin JO, Zabir AF, et al.
    Ann Thorac Surg, 2010 Jul;90(1):308-9.
    PMID: 20609810 DOI: 10.1016/j.athoracsur.2010.01.075
    An injury to the left ventricle after a chest tube insertion is a rare but lethal phenomenon that is likely to occur if precautions are not seriously addressed. We present a 15-year-old girl who was diagnosed a left empyema thoracis. An attempt to place a chest drain in this young girl was almost fatal. A left ventricular repair together with thoracotomy and decortication were successful. This case emphasizes the rarity of this lethal complication and the importance of the correct technique for chest tube insertion.
  17. Fulltext Toxic effect of high concentration of sonochemically synthesized polyvinylpyrrolidone-coated silver nanoparticles on Citrobacter sp. A1 and Enterococcus sp. C1
    Lau CP, Abdul-Wahab MF, Jaafar J, Chan GF, Abdul Rashid NA
    J Microbiol Immunol Infect, 2017 Aug;50(4):427-434.
    PMID: 26427880 DOI: 10.1016/j.jmii.2015.08.004
    BACKGROUND/PURPOSE: Currently, silver nanoparticles (AgNPs) have gained importance in various industrial applications. However, their impact upon release into the environment on microorganisms remains unclear. The aim of this study was to analyze the effect of polyvinylpyrrolidone-capped AgNPs synthesized in this laboratory on two bacterial strains isolated from the environment, Gram-negative Citrobacter sp. A1 and Gram-positive Enterococcus sp. C1.

    METHODS: Polyvinylpyrrolidone-capped AgNPs were synthesized by ultrasound-assisted chemical reduction. Characterization of the AgNPs involved UV-visible spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction, transmission electron microscopy, and energy dispersive X-ray spectroscopy. Citrobacter sp. A1 and Enterococcus sp. C1 were exposed to varying concentrations of AgNPs, and cell viability was determined. Scanning electron microscopy was performed to evaluate the morphological alteration of both species upon exposure to AgNPs at 1000 mg/L.

    RESULTS: The synthesized AgNPs were spherical in shape, with an average particle size of 15 nm. The AgNPs had different but prominent effects on either Citrobacter sp. A1 or Enterococcus sp. C1. At an AgNP concentration of 1000 mg/L, Citrobacter sp. A1 retained viability for 6 hours, while Enterococcus sp. C1 retained viability only for 3 hours. Citrobacter sp. A1 appeared to be more resistant to AgNPs than Enterococcus sp. C1. The cell wall of both strains was found to be morphologically altered at that concentration.

    CONCLUSION: Minute and spherical AgNPs significantly affected the viability of the two bacterial strains selected from the environment. Enterococcus sp. C1 was more vulnerable to AgNPs, probably due to its cell wall architecture and the absence of silver resistance-related genes.

  18. Fulltext Communal microaerophilic-aerobic biodegradation of Amaranth by novel NAR-2 bacterial consortium
    Chan GF, Rashid NA, Chua LS, Ab llah N, Nasiri R, Ikubar MR
    Bioresour Technol, 2012 Feb;105:48-59.
    PMID: 22182471 DOI: 10.1016/j.biortech.2011.11.094
    A novel bacterial consortium, NAR-2 which consists of Citrobacter freundii A1, Enterococcus casseliflavus C1 and Enterobacter cloacae L17 was investigated for biodegradation of Amaranth azo dye under sequential microaerophilic-aerobic condition. The NAR-2 bacterial consortium with E. casseliflavus C1 as the dominant strain enhanced the decolorization process resulting in reduction of Amaranth in 30 min. Further aerobic biodegradation, which was dominated by C. freundii A1 and E. cloacae L17, allowed biotransformation of azo reduction intermediates and mineralization via metabolic pathways including benzoyl-CoA, protocatechuate, salicylate, gentisate, catechol and cinnamic acid. The presence of autoxidation products which could be metabolized to 2-oxopentenoate was elucidated. The biodegradation mechanism of Amaranth by NAR-2 bacterial consortium was predicted to follow the steps of azo reduction, deamination, desulfonation and aromatic ring cleavage. This is for the first time the comprehensive microaerophilic-aerobic biotransformation pathways of Amaranth dye intermediates by bacterial consortium are being proposed.
  19. Quality improvement of spreadable processed cheese made from ultrafiltered milk retentates using commercial starter cultures
    El-Garhi HM, El-Aidie SA, Rashid NA, Hayee ZA
    Food Sci Technol Int, 2018 Sep;24(6):465-475.
    PMID: 29600878 DOI: 10.1177/1082013218766979
    This study was undertaken to evaluate the feasibility of using commercial starter cultures for quality improvement of spreadable processed cheese manufactured from ultrafiltered milk retentates. Compared to control, six samples of ultrafiltered milk retentate were incubated at 25 ℃ with starter cultures CHN-22, FRC-60, and ABT-8. Three samples were incubated for 24 h and the others were incubated for 72 h. Physicochemical, microbiological, and organoleptic characteristics in all treatments during the 90-day cold storage (6 ± 2 ℃) period were determined. The results showed that protein content of all treatments was significantly lower than the control. Utilization of starter cultures in ultrafiltered processed cheese production increased titratable acidity, where titratable acidity of the treatments (PC22-3, PC60-3, and PC8-3) was significantly higher than the other treatments and the control. PC8-1, PC60-1, and PC22-1 treatments were the highest penetrometer readings and with low firmness. All treatments had higher water soluble nitrogen/total nitrogen%, total bacterial viable and lactic acid bacterial counts especially PC22-3, PC60-3, and PC8-3 compared to the control. The results revealed that PC60-1 and PC22-3 treatments gained the highest acceptability scores than PC60-3, PC22-1, and the control.
  20. Protective Role of Natural Products in Cisplatin-Induced Nephrotoxicity
    Ridzuan NRA, Rashid NA, Othman F, Budin SB, Hussan F, Teoh SL
    Mini Rev Med Chem, 2019;19(14):1134-1143.
    PMID: 30894108 DOI: 10.2174/1389557519666190320124438
    Cisplatin is a widely used antineoplastic agent for the treatment of metastatic tumors, advanced bladder cancer and many other solid tumors. However, at higher doses, toxicities such as nephrotoxicity may appear. Cisplatin leads to DNA damage and subsequently renal cell death. Besides that, oxidative stress is also implicated as one of the main causes of nephrotoxicity. Several studies showed that numerous natural products: ginseng, curcumin, licorice, honey and pomegranate were able to reduce the oxidative stress by restoring the levels of antioxidant enzymes and also at the same time act as an anti-inflammatory agent. Furthermore, pre-treatment with vitamin supplementation, such as vitamin C, E and riboflavin markedly decreased serum urea and increased the levels of antioxidant enzymes in the kidney even after cisplatin induction in cancer patients. These natural products possess potent antioxidant and anti-inflammatory medicinal properties, and they can be safely used as a supplementary regime or combination therapy against cisplatin-induced nephrotoxicity. The present review focused on the protective role of a few natural products which is widely used in folk medicines in cisplatin-induced nephrotoxicity.
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