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Fulltext Andrographis paniculata leaf extract prevents thioacetamide-induced liver cirrhosis in rats

Abdulaziz Bardi D, Halabi MF, Hassandarvish P, Rouhollahi E, Paydar M, Moghadamtousi SZ, et al.

PLoS One, 2014;9(10):e109424.
PMID: 25280007 DOI: 10.1371/journal.pone.0109424

This study investigated the hepatoprotective effects of ethanolic Andrographis paniculata leaf extract (ELAP) on thioacetamide-induced hepatotoxicity in rats. An acute toxicity study proved that ELAP is not toxic in rats. To examine the effects of ELAP in vivo, male Sprague Dawley rats were given intraperitoneal injections of vehicle 10% Tween-20, 5 mL/kg (normal control) or 200 mg/kg TAA thioacetamide (to induce liver cirrhosis) three times per week. Three additional groups were treated with thioacetamide plus daily oral silymarin (50 mg/kg) or ELAP (250 or 500 mg/kg). Liver injury was assessed using biochemical tests, macroscopic and microscopic tissue analysis, histopathology, and immunohistochemistry. In addition, HepG2 and WRL-68 cells were treated in vitro with ELAP fractions to test cytotoxicity. Rats treated with ELAP exhibited significantly lower liver/body weight ratios and smoother, more normal liver surfaces compared with the cirrhosis group. Histopathology using Hematoxylin and Eosin along with Masson's Trichrome stain showed minimal disruption of hepatic cellular structure, minor fibrotic septa, a low degree of lymphocyte infiltration, and minimal collagen deposition after ELAP treatment. Immunohistochemistry indicated that ELAP induced down regulation of proliferating cell nuclear antigen. Also, hepatic antioxidant enzymes and oxidative stress parameters in ELAP-treated rats were comparable to silymarin-treated rats. ELAP administration reduced levels of altered serum liver biomarkers. ELAP fractions were non-cytotoxic to WRL-68 cells, but possessed anti-proliferative activity on HepG2 cells, which was confirmed by a significant elevation of lactate dehydrogenase, reactive oxygen species, cell membrane permeability, cytochrome c, and caspase-8,-9, and, -3/7 activity in HepG2 cells. A reduction of mitochondrial membrane potential was also detected in ELAP-treated HepG2 cells. The hepatoprotective effect of 500 mg/kg of ELAP is proposed to result from the reduction of thioacetamide-induced toxicity, normalizing reactive oxygen species levels, inhibiting cellular proliferation, and inducing apoptosis in HepG2 cells.
Fulltext Faculty development program assists the new faculty in constructing high-quality short answer questions; a quasi-experimental study

Abdulghani HM, Sattar K, Ahmad T, Akram A, Khalil MS

PLoS One, 2021;16(3):e0249319.
PMID: 33780493 DOI: 10.1371/journal.pone.0249319

Faculty development programs (FD) prepare the faculty for their educational role and career tasks. We aimed to evaluate the effectiveness of FDP in advancing the quality of short-answer questions (SAQs). This was a quasi-experimental study, comprising 37 new faculty. The SAQs were examined on psychometric analysis and Bloom's cognitive levels for the two educational blocks of 1st medical year (i.e. Musculoskeletal (MSK) and Renal blocks). We found substantial improvement in the discrimination index values of SAQs prepared after the workshop (p = 0.04). A higher number of SAQs with moderate difficulty and higher discrimination were also observed. Flaws within the post-workshop questions were reduced (3.0%) when compared with pre-workshop (12.5%). The major incline was also reported within Bloom's cognitive levels when pre-workshop K2 questions (30%) were compared with post-workshop (45.5%) with a p-value = 0.05. The SAQs constructed by the faculty member without participating in FDP are generally of unsatisfactory quality. After the FDP the assessment items of two blocks improved for various parameters of student assessment. The current study advocates that newly joined faculty shall be provided with the FDP to be guided, trained and supported for improving the quality of assessment through SAQs items writing.
Fulltext Secure Scientific Applications Scheduling Technique for Cloud Computing Environment Using Global League Championship Algorithm

Abdulhamid SM, Abd Latiff MS, Abdul-Salaam G, Hussain Madni SH

PLoS One, 2016;11(7):e0158102.
PMID: 27384239 DOI: 10.1371/journal.pone.0158102

Cloud computing system is a huge cluster of interconnected servers residing in a datacenter and dynamically provisioned to clients on-demand via a front-end interface. Scientific applications scheduling in the cloud computing environment is identified as NP-hard problem due to the dynamic nature of heterogeneous resources. Recently, a number of metaheuristics optimization schemes have been applied to address the challenges of applications scheduling in the cloud system, without much emphasis on the issue of secure global scheduling. In this paper, scientific applications scheduling techniques using the Global League Championship Algorithm (GBLCA) optimization technique is first presented for global task scheduling in the cloud environment. The experiment is carried out using CloudSim simulator. The experimental results show that, the proposed GBLCA technique produced remarkable performance improvement rate on the makespan that ranges between 14.44% to 46.41%. It also shows significant reduction in the time taken to securely schedule applications as parametrically measured in terms of the response time. In view of the experimental results, the proposed technique provides better-quality scheduling solution that is suitable for scientific applications task execution in the Cloud Computing environment than the MinMin, MaxMin, Genetic Algorithm (GA) and Ant Colony Optimization (ACO) scheduling techniques.
Fulltext An evolutionary firefly algorithm for the estimation of nonlinear biological model parameters

Abdullah A, Deris S, Anwar S, Arjunan SN

PLoS One, 2013;8(3):e56310.
PMID: 23469172 DOI: 10.1371/journal.pone.0056310

The development of accurate computational models of biological processes is fundamental to computational systems biology. These models are usually represented by mathematical expressions that rely heavily on the system parameters. The measurement of these parameters is often difficult. Therefore, they are commonly estimated by fitting the predicted model to the experimental data using optimization methods. The complexity and nonlinearity of the biological processes pose a significant challenge, however, to the development of accurate and fast optimization methods. We introduce a new hybrid optimization method incorporating the Firefly Algorithm and the evolutionary operation of the Differential Evolution method. The proposed method improves solutions by neighbourhood search using evolutionary procedures. Testing our method on models for the arginine catabolism and the negative feedback loop of the p53 signalling pathway, we found that it estimated the parameters with high accuracy and within a reasonable computation time compared to well-known approaches, including Particle Swarm Optimization, Nelder-Mead, and Firefly Algorithm. We have also verified the reliability of the parameters estimated by the method using an a posteriori practical identifiability test.
Fulltext Prevalence of limited health literacy among patients with type 2 diabetes mellitus: A systematic review

Abdullah A, Liew SM, Salim H, Ng CJ, Chinna K

PLoS One, 2019;14(5):e0216402.
PMID: 31063470 DOI: 10.1371/journal.pone.0216402

BACKGROUND: Health literacy (HL) skills are essential to enable self-management and shared decision-making in patients with type 2 diabetes mellitus (T2DM). Limited HL in these patients is associated with poorer outcomes. It is not clear what the burden of limited HL in patients with T2DM across countries and what factors influence it.
METHODS: A systematic review was conducted according to the PRISMA guidelines. The study protocol was registered with PROSPERO (CRD42017056150). We searched MEDLINE, EMBASE, PsycINFO, CINAHL and ERIC for articles published up to January 2017. Articles that measured HL levels in adult patients with T2DM; that used validated HL tools; and that were reported in English were included. Two reviewers assessed studies for eligibility and quality, and extracted the data. Prevalence of limited HL is calculated from the number of patients with less than adequate HL over the total number of patients with T2DM in the study. Meta-analysis and meta-regression analysis were conducted using the Open Meta-analyst software.
RESULTS: Twenty-nine studies involving 13,457 patients with T2DM from seven countries were included. In total, seven different HL measurement tools were used. The prevalence of limited HL ranged from 7.3% to 82%, lowest in Switzerland and the highest in Taiwan. Meta-regression analysis of all included studies showed the country of study (p<0.001), HL tool used (p = 0.002), and the country's region (p<0.001) contributed to the variation findings. Thirteen studies in the USA measured functional HL. The pooled prevalence of inadequate functional HL among patients with T2DM in the USA was 28.9% (95% CI: 20.4-37.3), with high heterogeneity (I2 = 97.9%, p <0.001). Studies were done in the community as opposed to a hospital or primary care (p = 0.005) and populations with education level lower than high school education (p = 0.009) reported a higher prevalence of limited HL.
CONCLUSION: The prevalence of limited HL in patients with T2DM varied widely between countries, HL tools used and the country's region. Pooled prevalence showed nearly one in three patients with T2DM in the USA had limited functional HL. Interactions with healthcare providers and educational attainment were associated with reported of prevalence in the USA.
Fulltext An improved swarm optimization for parameter estimation and biological model selection

Abdullah A, Deris S, Mohamad MS, Anwar S

PLoS One, 2013;8(4):e61258.
PMID: 23593445 DOI: 10.1371/journal.pone.0061258

One of the key aspects of computational systems biology is the investigation on the dynamic biological processes within cells. Computational models are often required to elucidate the mechanisms and principles driving the processes because of the nonlinearity and complexity. The models usually incorporate a set of parameters that signify the physical properties of the actual biological systems. In most cases, these parameters are estimated by fitting the model outputs with the corresponding experimental data. However, this is a challenging task because the available experimental data are frequently noisy and incomplete. In this paper, a new hybrid optimization method is proposed to estimate these parameters from the noisy and incomplete experimental data. The proposed method, called Swarm-based Chemical Reaction Optimization, integrates the evolutionary searching strategy employed by the Chemical Reaction Optimization, into the neighbouring searching strategy of the Firefly Algorithm method. The effectiveness of the method was evaluated using a simulated nonlinear model and two biological models: synthetic transcriptional oscillators, and extracellular protease production models. The results showed that the accuracy and computational speed of the proposed method were better than the existing Differential Evolution, Firefly Algorithm and Chemical Reaction Optimization methods. The reliability of the estimated parameters was statistically validated, which suggests that the model outputs produced by these parameters were valid even when noisy and incomplete experimental data were used. Additionally, Akaike Information Criterion was employed to evaluate the model selection, which highlighted the capability of the proposed method in choosing a plausible model based on the experimental data. In conclusion, this paper presents the effectiveness of the proposed method for parameter estimation and model selection problems using noisy and incomplete experimental data. This study is hoped to provide a new insight in developing more accurate and reliable biological models based on limited and low quality experimental data.
Fulltext Polyesters Based on Linoleic Acid for Biolubricant Basestocks: Low-Temperature, Tribological and Rheological Properties

Abdullah BM, Zubairi SI, Huri HZ, Hairunisa N, Yousif E, Basu RC

PLoS One, 2016;11(3):e0151603.
PMID: 27008312 DOI: 10.1371/journal.pone.0151603

Presently, plant oils which contain high percentage of linoleic acid 1 are perceived to be a viable alternative to mineral oil for biolubricant applications due to their biodegradability and technical properties. In order to get biodegradable lubricant, triester derivatives compounds (1-5) were synthesized and characterized. The processes involved were monoepoxidation of linoleic acid 2, oxirane ring opening 3, esterification 4 and acylation 5. The structures of the products were confirmed by FTIR, 1H and 13C-NMR and LC-MS. The results that showed lowest temperature properties were obtained for triester 5, with a pour point value (PP) of -73°C, highest onset temperature (260°C) and lowest volatility at 0.30%. Viscosity index (VI) increased for the ester's synthetic compounds (2, 3, 4, 5), while the PP decreased. This behavior is the result of the increase of the chain length of the branching agents. Triester based linoleic acid has improved properties such as low-temperature and tribological properties. These results will make it feasible for plant oil to be used for biolubricants, fuels in chain saws, transmission oil and brake fluid.
Fulltext The antibacterial efficacy of silver diamine fluoride (SDF) is not modulated by potassium iodide (KI) supplements: A study on in-situ plaque biofilms using viability real-time PCR with propidium monoazide

Abdullah N, Al Marzooq F, Mohamad S, Abd Rahman N, Rani KGA, Chi Ngo H, et al.

PLoS One, 2020;15(11):e0241519.
PMID: 33141868 DOI: 10.1371/journal.pone.0241519

Silver diamine fluoride (SDF) is commonly used to arrest caries lesions, especially in early childhood caries. Recently, it was suggested that SDF can be combined with potassium iodide (KI) to minimize the discoloration of demineralized dentine associated with SDF application. However, the antibacterial efficacy of SDF alone or combined with KI on in-situ biofilm is unknown. Hence, we compared the anti-plaque biofilm efficacy of two different commercially available SDF solutions, with or without KI, using an in-situ biofilm, analysed using viability real-time PCR with propidium monoazide (PMA). Appliance-borne in-situ biofilm samples (n = 90) were grown for a period of 6 h in five healthy subjects who repeated the experiment on three separate occasions, using a validated, novel, intraoral device. The relative anti-biofilm efficacy of two SDF formulations; 38.0% Topamine (SDFT) and 31.3%, Riva Star (SDFR), KI alone, and KI in combination with SDFR (SDFR+KI) was compared. The experiments were performed by applying an optimized volume of the agents onto the biofilm for 1min, mimicking the standard clinical procedure. Afterwards the viability of the residual biofilm bacteria was quantified using viability real-time PCR with PMA, then the percentage of viable from total bacteria was calculated. Both SDF formulations (SDFT and SDFR) exhibited potent antibacterial activities against the in-situ biofilm; however, there was non-significant difference in their efficacy. KI alone did not demonstrate any antibacterial effect, and there was non-significant difference in the antibacterial efficacy of SDF alone compared to SDF with KI, (SDFT v SDFR/KI). Thus, we conclude that the antibacterial efficacy of SDF against plaque biofilms is not modulated by KI supplements. Viability real-time PCR with PMA was successfully used to analyze the viability of naturally grown oral biofilm; thus, the same method can be used to test the antimicrobial effect of other agents on oral biofilms in future research.
Fulltext Plasmodium vivax population structure and transmission dynamics in Sabah Malaysia

Abdullah NR, Barber BE, William T, Norahmad NA, Satsu UR, Muniandy PK, et al.

PLoS One, 2013;8(12):e82553.
PMID: 24358203 DOI: 10.1371/journal.pone.0082553

Despite significant progress in the control of malaria in Malaysia, the complex transmission dynamics of P. vivax continue to challenge national efforts to achieve elimination. To assess the impact of ongoing interventions on P. vivax transmission dynamics in Sabah, we genotyped 9 short tandem repeat markers in a total of 97 isolates (8 recurrences) from across Sabah, with a focus on two districts, Kota Marudu (KM, n = 24) and Kota Kinabalu (KK, n = 21), over a 2 year period. STRUCTURE analysis on the Sabah-wide dataset demonstrated multiple sub-populations. Significant differentiation (F ST = 0.243) was observed between KM and KK, located just 130 Km apart. Consistent with low endemic transmission, infection complexity was modest in both KM (mean MOI = 1.38) and KK (mean MOI = 1.19). However, population diversity remained moderate (H E = 0.583 in KM and H E = 0.667 in KK). Temporal trends revealed clonal expansions reflecting epidemic transmission dynamics. The haplotypes of these isolates declined in frequency over time, but persisted at low frequency throughout the study duration. A diverse array of low frequency isolates were detected in both KM and KK, some likely reflecting remnants of previous expansions. In accordance with clonal expansions, high levels of Linkage Disequilibrium (I A (S) >0.5 [P<0.0001] in KK and KM) declined sharply when identical haplotypes were represented once (I A (S) = 0.07 [P = 0.0076] in KM, and I A (S) = -0.003 [P = 0.606] in KK). All 8 recurrences, likely to be relapses, were homologous to the prior infection. These recurrences may promote the persistence of parasite lineages, sustaining local diversity. In summary, Sabah's shrinking P. vivax population appears to have rendered this low endemic setting vulnerable to epidemic expansions. Migration may play an important role in the introduction of new parasite strains leading to epidemic expansions, with important implications for malaria elimination.
Fulltext Pre-induction cervical assessment using transvaginal ultrasound versus Bishops cervical scoring as predictors of successful induction of labour in term pregnancies: A hospital-based comparative clinical trial

Abdullah ZHA, Chew KT, Velayudham VRV, Yahaya Z, Jamil AAM, Abu MA, et al.

PLoS One, 2022;17(1):e0262387.
PMID: 35081157 DOI: 10.1371/journal.pone.0262387

OBJECTIVE: To evaluate the association between transvaginal ultrasound scan of cervix and Bishop's score in predicting successful induction of labour, cut-off points and patients' tolerability and acceptance for both procedures.
DESIGN: A comparative clinical trial.
SETTING: A tertiary hospital in Selangor, Malaysia.
PARTICIPANTS: 294 women planned for elective induction of labour for various indications were included. All women had transvaginal ultrasound to assess the cervical length and digital vaginal examination to assess the Bishop cervical scoring by separate investigators before induction of labour.
PRIMARY OUTCOME MEASURE: To evaluate the association of the cervical length by transvaginal ultrasound scan and Bishop score in predicting successful induction of labour.
SECONDARY OUTCOME MEASURE: Variables associated with successful induction of labour and patients' tolerability and acceptance for transvaginal ultrasound scan of cervix.
RESULTS: There was no statistically significant difference among the vaginal and Caesarean delivery groups in terms of mean maternal age, height, weight, body mass index, ethnicity and gestational age at induction. Vaginal delivery occurred in 207 women (70.4%) and 87 women (29.6%) delivered via Caesarean section. There was a high degree of correlation between the cervical length and Bishop score (r-value 0.745; p <0.001). Sonographic assessment of cervical length demonstrated a comparable accuracy in comparison to Bishop score. Analysis using ROC curves noted an optimal cut-off value of ≤27mm for cervical length and Bishop score of ≥ 4, with a sensitivity of 69.1% vs 67%, specificity 60.9% vs 55%, and area under the curves (AUCs) of 0.672 and 0.643 respectively (p <0.001). Multivariate logistic regression analysis demonstrated that parity (OR 2.70), cervical length (OR 0.925), Bishop score (OR 1.272) and presence of funnelling (OR 3.292) were highly significant as independent predictors of success labour induction. Women also expressed significantly less discomfort with transvaginal ultrasound compared with digital vaginal examination.
CONCLUSION: Sonographic assessment of cervical measurement predicts the success of induction of labour with similar diagnostic accuracy with conventional Bishop score.
Fulltext Hybrid Symbiotic Organisms Search Optimization Algorithm for Scheduling of Tasks on Cloud Computing Environment

Abdullahi M, Ngadi MA

PLoS One, 2016;11(6):e0158229.
PMID: 27348127 DOI: 10.1371/journal.pone.0158229

Cloud computing has attracted significant attention from research community because of rapid migration rate of Information Technology services to its domain. Advances in virtualization technology has made cloud computing very popular as a result of easier deployment of application services. Tasks are submitted to cloud datacenters to be processed on pay as you go fashion. Task scheduling is one the significant research challenges in cloud computing environment. The current formulation of task scheduling problems has been shown to be NP-complete, hence finding the exact solution especially for large problem sizes is intractable. The heterogeneous and dynamic feature of cloud resources makes optimum task scheduling non-trivial. Therefore, efficient task scheduling algorithms are required for optimum resource utilization. Symbiotic Organisms Search (SOS) has been shown to perform competitively with Particle Swarm Optimization (PSO). The aim of this study is to optimize task scheduling in cloud computing environment based on a proposed Simulated Annealing (SA) based SOS (SASOS) in order to improve the convergence rate and quality of solution of SOS. The SOS algorithm has a strong global exploration capability and uses fewer parameters. The systematic reasoning ability of SA is employed to find better solutions on local solution regions, hence, adding exploration ability to SOS. Also, a fitness function is proposed which takes into account the utilization level of virtual machines (VMs) which reduced makespan and degree of imbalance among VMs. CloudSim toolkit was used to evaluate the efficiency of the proposed method using both synthetic and standard workload. Results of simulation showed that hybrid SOS performs better than SOS in terms of convergence speed, response time, degree of imbalance, and makespan.
Fulltext Optimisation of the Photonic Efficiency of TiO2 Decorated on MWCNTs for Methylene Blue Photodegradation

Abdullahi N, Saion E, Shaari AH, Al-Hada NM, Keiteb A

PLoS One, 2015;10(5):e0125511.
PMID: 25993127 DOI: 10.1371/journal.pone.0125511

MWCNTs/TiO2 nanocomposite was prepared by oxidising MWCNT in H2SO4/HNO3 then decorating it with TiO2-p25 nanopowder. The composites were characterised using XRD, TEM, FT-IR PL and UV-vis spectroscopy. The TEM images have shown TiO2 nanoparticles immobilised onto the sidewalls of the MWCNTs. The UV-vis spectrum confirms that the nanocomposites can significantly absorb more light in the visible regions compared with the commercial TiO2 (P25). The catalytic activity of these nanocomposites was determined by photooxidation of MB aqueous solution in the presence of visible light. The MWCNTs/TiO2 (1:3) mass ratio showed maximum degradation efficiency. However, its activity was more favourable in alkaline and a neutral pH than an acidic medium.
Fulltext Mobile phone reminders and peer counseling improve adherence and treatment outcomes of patients on ART in Malaysia: A randomized clinical trial

Abdulrahman SA, Rampal L, Ibrahim F, Radhakrishnan AP, Kadir Shahar H, Othman N

PLoS One, 2017;12(5):e0177698.
PMID: 28520768 DOI: 10.1371/journal.pone.0177698

BACKGROUND: Adherence to treatment remains the cornerstone of long term viral suppression and successful treatment outcomes among patients receiving Antiretroviral Therapy (ART).
OBJECTIVE(S): Evaluate the effectiveness of mobile phone reminders and peer counseling in improving adherence and treatment outcomes among HIV positive patients on ART in Malaysia.
METHODS: A single-blind, parallel group RCT conducted in Hospital Sungai Buloh, Malaysia in which 242 adult Malaysian patients were randomized to intervention or control groups. Intervention consisted of a reminder module delivered through SMS and telephone call reminders by trained research assistants for 24 consecutive weeks (starting from date of ART initiation), in addition to adherence counseling at every clinic visit. The length of intended follow up for each patient was 6 months. Data on adherence behavior of patients was collected using specialized, pre-validated Adult AIDS Clinical Trial Group (AACTG) adherence questionnaires. Data on weight, clinical symptoms, CD4 count and viral load tests were also collected. Data was analyzed using SPSS version 22 and R software. Repeated measures ANOVA, Friedman's ANOVA and Multivariate regression models were used to evaluate efficacy of the intervention.
RESULTS: The response rate after 6 months follow up was 93%. There were no significant differences at baseline in gender, employment status, income distribution and residential location of respondents between the intervention and control group. After 6 months follow up, the mean adherence was significantly higher in the intervention group (95.7; 95% CI: 94.39-96.97) as compared to the control group (87.5; 95% CI: 86.14-88.81). The proportion of respondents who had Good (>95%) adherence was significantly higher in the intervention group (92.2%) compared to the control group (54.6%). A significantly lower frequency in missed appointments (14.0% vs 35.5%) (p = 0.001), lower viral load (p = 0.001), higher rise in CD4 count (p = 0.017), lower incidence of tuberculosis (p = 0.001) and OIs (p = 0.001) at 6 months follow up, was observed among patients in the intervention group.
CONCLUSION: Mobile phone reminders (SMS and telephone call reminders) and peer counseling are effective in improving adherence and treatment outcomes among HIV positive patients on ART in Malaysia. These findings may be of potential benefit for collaborative adherence planning between patients and health care providers at ART commencement.
Fulltext Subtype distribution of Blastocystis isolates in Sebha, Libya

Abdulsalam AM, Ithoi I, Al-Mekhlafi HM, Al-Mekhlafi AM, Ahmed A, Surin J

PLoS One, 2013;8(12):e84372.
PMID: 24376805 DOI: 10.1371/journal.pone.0084372

BACKGROUND: Blastocystis is a genetically diverse and a common intestinal parasite of humans with a controversial pathogenic potential. This study was carried out to identify the Blastocystis subtypes and their association with demographic and socioeconomic factors among outpatients living in Sebha city, Libya.
METHODS/FINDINGS: Blastocystis in stool samples were cultured followed by isolation, PCR amplification of a partial SSU rDNA gene, cloning, and sequencing. The DNA sequences of isolated clones showed 98.3% to 100% identity with the reference Blastocystis isolates from the Genbank. Multiple sequence alignment showed polymorphism from one to seven base substitution and/or insertion/deletion in several groups of non-identical nucleotides clones. Phylogenetic analysis revealed three assemblage subtypes (ST) with ST1 as the most prevalent (51.1%) followed by ST2 (24.4%), ST3 (17.8%) and mixed infections of two concurrent subtypes (6.7%).
BLASTOCYSTIS: ST1 infection was significantly associated with female (P = 0.009) and low educational level (P = 0.034). ST2 was also significantly associated with low educational level (P= 0.008) and ST3 with diarrhoea (P = 0.008).
CONCLUSION: Phylogenetic analysis of Libyan Blastocystis isolates identified three different subtypes; with ST1 being the predominant subtype and its infection was significantly associated with female gender and low educational level. More extensive studies are needed in order to relate each Blastocystis subtype with clinical symptoms and potential transmission sources in this community.
Fulltext Harmony Search Algorithm for Word Sense Disambiguation

Abed SA, Tiun S, Omar N

PLoS One, 2015;10(9):e0136614.
PMID: 26422368 DOI: 10.1371/journal.pone.0136614

Word Sense Disambiguation (WSD) is the task of determining which sense of an ambiguous word (word with multiple meanings) is chosen in a particular use of that word, by considering its context. A sentence is considered ambiguous if it contains ambiguous word(s). Practically, any sentence that has been classified as ambiguous usually has multiple interpretations, but just one of them presents the correct interpretation. We propose an unsupervised method that exploits knowledge based approaches for word sense disambiguation using Harmony Search Algorithm (HSA) based on a Stanford dependencies generator (HSDG). The role of the dependency generator is to parse sentences to obtain their dependency relations. Whereas, the goal of using the HSA is to maximize the overall semantic similarity of the set of parsed words. HSA invokes a combination of semantic similarity and relatedness measurements, i.e., Jiang and Conrath (jcn) and an adapted Lesk algorithm, to perform the HSA fitness function. Our proposed method was experimented on benchmark datasets, which yielded results comparable to the state-of-the-art WSD methods. In order to evaluate the effectiveness of the dependency generator, we perform the same methodology without the parser, but with a window of words. The empirical results demonstrate that the proposed method is able to produce effective solutions for most instances of the datasets used.
Fulltext Radiolytic formation of Fe3O4 nanoparticles: influence of radiation dose on structure and magnetic properties

Abedini A, Daud AR, Abdul Hamid MA, Kamil Othman N

PLoS One, 2014;9(3):e90055.
PMID: 24608715 DOI: 10.1371/journal.pone.0090055

Colloidal Fe3O4 nanoparticles were synthesized using a gamma-radiolysis method in an aqueous solution containing iron chloride in presence of polyvinyl alcohol and isopropanol as colloidal stabilizer and hydroxyl radical scavenger, respectively. Gamma irradiation was carried out in a 60Co gamma source chamber at different absorbed doses. Increasing the radiation dose above a certain critical dose (100 kGy) leads to particle agglomeration enhancement, and this can influence the structure and crystallinity, and consequently the magnetic properties of the resultant particles. The optimal condition for formation of Fe3O4 nanoparticles with a uniform and narrow size distribution occurred at a dose of 100 kGy, as confirmed by X-ray diffractometry and transmission electron microscopy. A vibrating sample magnetometry study showed that, when radiation dose increased, the saturation and remanence magnetization decreased, whereas the coercivity and the remanence ratio increased. This magnetic behavior results from variations in crystallinity, surface effects, and particle size effects, which are all dependent on the radiation dose. In addition, Fourier transform infrared spectroscopy was performed to investigate the nature of the bonds formed between the polymer chains and the metal surface at different radiation doses.
Fulltext Genetic diversity of Pantoea stewartii subspecies stewartii causing jackfruit-bronzing disease in Malaysia

Abidin N, Ismail SI, Vadamalai G, Yusof MT, Hakiman M, Karam DS, et al.

PLoS One, 2020;15(6):e0234350.
PMID: 32530926 DOI: 10.1371/journal.pone.0234350

Jackfruit-bronzing is caused by bacteria Pantoea stewartii subspecies stewartii (P. stewartii subsp. stewartii), showing symptoms of yellowish-orange to reddish discolouration and rusty specks on pulps and rags of jackfruit. Twenty-eight pure bacterial strains were collected from four different jackfruit outbreak collection areas in Peninsular Malaysia (Jenderam, Maran, Muadzam Shah and Ipoh). Positive P. stewartii subsp. stewartii verification obtained in the study was based on the phenotypic, hypersensitivity, pathogenicity and molecular tests. Multilocus sequence analysis (MLSA) was performed using four housekeeping genes (gyrB, rpoB, atpD and infB) on all 28 bacterial strains. Single gyrB, rpoB, atpD and infB phylogenetic trees analyses revealed the bootstrap value of 99-100% between our bacterial strains with P. stewartii subsp. stewartii reference strains and P. stewartii subsp. indologenes reference strains. On the other hand, phylogenetic tree of the concatenated sequences of the four housekeeping genes revealed that our 28 bacterial strains were more closely related to P. stewartii subsp. stewartii (99% similarities) compared to its close relative P. stewartii subsp. indologenes, although sequence similarity between these two subspecies were up to 100%. All the strains collected from the four collection areas clustered together, pointing to no variation among the bacterial strains. This study improves our understanding and provided new insight on the genetic diversity of P. stewartii subsp. stewartii associated with jackfruit-bronzing in Malaysia.
Fulltext Combating obesity through healthy eating behavior: a call for system dynamics optimization

Abidin NZ, Mamat M, Dangerfield B, Zulkepli JH, Baten MA, Wibowo A

PLoS One, 2014;9(12):e114135.
PMID: 25502170 DOI: 10.1371/journal.pone.0114135

Poor eating behavior has been identified as one of the core contributory factors of the childhood obesity epidemic. The consequences of obesity on numerous aspects of life are thoroughly explored in the existing literature. For instance, evidence shows that obesity is linked to incidences of diseases such as heart disease, type-2 diabetes, and some cancers, as well as psychosocial problems. To respond to the increasing trends in the UK, in 2008 the government set a target to reverse the prevalence of obesity (POB) back to 2000 levels by 2020. This paper will outline the application of system dynamics (SD) optimization to simulate the effect of changes in the eating behavior of British children (aged 2 to 15 years) on weight and obesity. This study also will identify how long it will take to achieve the government's target. This paper proposed a simulation model called Intervention Childhood Obesity Dynamics (ICOD) by focusing the interrelations between various strands of knowledge in one complex human weight regulation system. The model offers distinct insights into the dynamics by capturing the complex interdependencies from the causal loop and feedback structure, with the intention to better understand how eating behaviors influence children's weight, body mass index (BMI), and POB measurement. This study proposed a set of equations that are revised from the original (baseline) equations. The new functions are constructed using a RAMP function of linear decrement in portion size and number of meal variables from 2013 until 2020 in order to achieve the 2020 desired target. Findings from the optimization analysis revealed that the 2020 target won't be achieved until 2026 at the earliest, six years late. Thus, the model suggested that a longer period may be needed to significantly reduce obesity in this population.
Fulltext Dengue in Dhaka, Bangladesh: Hospital-based cross-sectional KAP assessment at Dhaka North and Dhaka South City Corporation area

Abir T, Ekwudu O, Kalimullah NA, Nur-A Yazdani DM, Al Mamun A, Basak P, et al.

PLoS One, 2021;16(3):e0249135.
PMID: 33784366 DOI: 10.1371/journal.pone.0249135

Dengue, the most important mosquito-borne viral disease of humans is a recurring global health problem. In Bangladesh, dengue outbreaks are on the increase despite the efforts of government and it is not clear what the understanding of the general Dhaka population towards dengue fever is. Knowledge, attitude and practice (KAP) studies are essential guides in public health interventions. Hence, using KAP, this study aims to assess patient-perspectives with regards to factors associated with dengue, as well as investigate the associated factors between the two corporations in Dhaka. A Hospital-based cross-sectional study of 242 fever patients from two city-corporations in Dhaka (Dhaka North City Corporations, DNCC (n = 91, 37.6%) and Dhaka South City Corporation, DSCC (n = 151, 62.4%) was conducted using pre-tested KAP items. Wilcoxon's Rank Sum was used to determine the KAP by DNCC, DSCC and both corporations and multivariate Poisson regression analyses. The two corporations were analysed separately due to the differences in income distribution, concentration of slums, hospitals and clinics. The study found that more than half of the study population were knowledgeable about dengue (mean percentage scores was 52%), possess an appropriate and acceptable attitude towards the disease (69.2%), and about two thirds of the respondents (71.4%) engaged in practices towards its prevention. After adjusting for the potential cofounders, the factors associated with KAP about dengue fever varied between DNCC and DSCC; with duration of residency and use of mosquito nets were associated with knowledge in the north while income class and age were associated with knowledge and attitude in the south. In the pooled analysis (combining both corporations), knowledge of dengue was associated with good practice towards dengue fever among the respondents. The duration of residence in Dhaka (10+ years), not using mosquito nets and length of time spent in the hospital (7+ days) due to dengue, and decreased knowledge (Adjusted coefficient (β) = -0.01, 95%CI: -0.02, -0.01) were associated with attitude towards dengue in DNCC. On the other hand, middle-high income class, age (40+ years) and increased knowledge were associated with practice towards dengue in DSCC (β = 0.02, 95%CI: 0.01, 0.03). Efforts to increase knowledge about dengue fever through education by the administrations of both corporations would benefit from targeting these high-risk groups for a more sustainable outcome.
Fulltext Brinjal leaf diseases detection based on discrete Shearlet transform and Deep Convolutional Neural Network

Abisha S, Mutawa AM, Murugappan M, Krishnan S

PLoS One, 2023;18(4):e0284021.
PMID: 37018344 DOI: 10.1371/journal.pone.0284021

Different diseases are observed in vegetables, fruits, cereals, and commercial crops by farmers and agricultural experts. Nonetheless, this evaluation process is time-consuming, and initial symptoms are primarily visible at microscopic levels, limiting the possibility of an accurate diagnosis. This paper proposes an innovative method for identifying and classifying infected brinjal leaves using Deep Convolutional Neural Networks (DCNN) and Radial Basis Feed Forward Neural Networks (RBFNN). We collected 1100 images of brinjal leaf disease that were caused by five different species (Pseudomonas solanacearum, Cercospora solani, Alternaria melongenea, Pythium aphanidermatum, and Tobacco Mosaic Virus) and 400 images of healthy leaves from India's agricultural form. First, the original plant leaf is preprocessed by a Gaussian filter to reduce the noise and improve the quality of the image through image enhancement. A segmentation method based on expectation and maximization (EM) is then utilized to segment the leaf's-diseased regions. Next, the discrete Shearlet transform is used to extract the main features of the images such as texture, color, and structure, which are then merged to produce vectors. Lastly, DCNN and RBFNN are used to classify brinjal leaves based on their disease types. The DCNN achieved a mean accuracy of 93.30% (with fusion) and 76.70% (without fusion) compared to the RBFNN (82%-without fusion, 87%-with fusion) in classifying leaf diseases.

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