Browse publications by year: 2018

  1. Tai HK, Jusoh SA, Siu SWI
    J Cheminform, 2018 Dec 14;10(1):62.
    PMID: 30552524 DOI: 10.1186/s13321-018-0320-9
    BACKGROUND: Protein-ligand docking programs are routinely used in structure-based drug design to find the optimal binding pose of a ligand in the protein's active site. These programs are also used to identify potential drug candidates by ranking large sets of compounds. As more accurate and efficient docking programs are always desirable, constant efforts focus on developing better docking algorithms or improving the scoring function. Recently, chaotic maps have emerged as a promising approach to improve the search behavior of optimization algorithms in terms of search diversity and convergence speed. However, their effectiveness on docking applications has not been explored. Herein, we integrated five popular chaotic maps-logistic, Singer, sinusoidal, tent, and Zaslavskii maps-into PSOVina[Formula: see text], a recent variant of the popular AutoDock Vina program with enhanced global and local search capabilities, and evaluated their performances in ligand pose prediction and virtual screening using four docking benchmark datasets and two virtual screening datasets.

    RESULTS: Pose prediction experiments indicate that chaos-embedded algorithms outperform AutoDock Vina and PSOVina in ligand pose RMSD, success rate, and run time. In virtual screening experiments, Singer map-embedded PSOVina[Formula: see text] achieved a very significant five- to sixfold speedup with comparable screening performances to AutoDock Vina in terms of area under the receiver operating characteristic curve and enrichment factor. Therefore, our results suggest that chaos-embedded PSOVina methods might be a better option than AutoDock Vina for docking and virtual screening tasks. The success of chaotic maps in protein-ligand docking reveals their potential for improving optimization algorithms in other search problems, such as protein structure prediction and folding. The Singer map-embedded PSOVina[Formula: see text] which is named PSOVina-2.0 and all testing datasets are publicly available on https://cbbio.cis.umac.mo/software/psovina .

    MeSH terms: Algorithms; Ligands; Proteins; ROC Curve; Drug Design; Benchmarking; Catalytic Domain; Singing
  2. Muid, S., Hamid, Z., Nawawi, H.
    MyJurnal
    The beneficial effects of Palm Tocotrienol Rich Fraction (TRF) in the reduction of cholesterol and oxidative stress in human especially in Non-Familial Hypercholesterolaemia (NFH) patients are still lacking and need to be further investigated. In this clinical trial, 37 NFH patients were recruited and randomized to either Palmvitee (60 mg/day TRF) [NFHe; n= 12) and atorvastatin 10 mg/day (NFHs; n=25). Fasting serum lipids, F2 -isoprostanes, oxidized LDL (ox-LDL) and malondialdehyde (MDA) were measured at baseline (BL), 2 weeks and 12 weeks. NFHe group showed significant reduction in Total cholesterol, TC, LDL, MDA, F2 – isoprostanes and ox-LDL at 12 weeks compared to BL. NFHs group showed a reduction in TC, LDL and TG, MDA and F2 – isoprostanes in 12 weeks compared to the BL. NFHs had greater % change reduction of TC, LDL, TG and MDA than NFHe in 12 weeks. Despite that, NFHe and NFHs had comparable % reduction of F2–isoprostanes in 12 weeks. NFHe had greater % change reduction of ox-LDL than NFHs. In conclusion, TRF reduces cholesterol level in NFH patients even though it is not as efficient as statins. The ability of TRF in the reduction of oxidative stress especially F2-isoprostanes is comparable with statins. TRF has a great potential in the prevention of atherosclerosis in part not only due to its cholesterol lowering activity, but perhaps more effective as a potent antioxidant.
  3. Tuan Mohamood NFA, Zainuddin N, Ahmad Ayob M, Tan SW
    Chem Cent J, 2018 Dec 06;12(1):133.
    PMID: 30523481 DOI: 10.1186/s13065-018-0500-8
    In this study, sago starch was modified in order to enhance its physicochemical properties. Carboxymethylation was used to introduce a carboxymethyl group into a starch compound. The carboxymethyl sago starch (CMSS) was used to prepare smart hydrogel by adding acetic acid into the CMSS powder as the crosslinking agent. The degree of substitution of the CMSS obtained was 0.6410. The optimization was based on the gel content and degree of swelling of the hydrogel. In this research, four parameters were studied in order to optimize the formation of CMSS-acid hydrogel. The parameters were; CMSS concentration, acetic acid concentration, reaction time and reaction temperature. From the data analyzed, 76.69% of optimum gel content was obtained with 33.77 g/g of degree of swelling. Other than that, the swelling properties of CMSS-acid hydrogel in different media such as salt solution, different pH of phosphate buffer saline solution as well as acidic and alkaline solution were also investigated. The results showed that the CMSS-acid hydrogel swelled in both alkaline and salt solution, while in acidic or low pH solution, it tended to shrink and deswell. The production of the hydrogel as a smart material offers a lot of auspicious benefits in the future especially related to swelling behaviour and properties of the hydrogel in different types of media.
    MeSH terms: Phosphates; Reaction Time; Sodium Chloride; Starch; Temperature; Sodium Chloride, Dietary; Acetic Acid
  4. Zheng X, Liao Y, Wang J, Hu S, Rudramurthy GR, Swamy MK, et al.
    PMID: 30524484 DOI: 10.1155/2018/9691085
    Microglial cells, upon hyperactivation, produce proinflammatory cytokines and other oxidative stress mediators causing neuroinflammation, which is associated with the progress of many neurodegenerative diseases. Suppressing the microglial activation has hence been used as an approach for treating such diseases. In this study, the antineuroinflammatory effect of simvastatin was examined in lipopolysaccharide (LPS)-activated rat C6 glioma cells. The cell proliferation and cytotoxic effect of LPS and simvastatin on C6 glioma cells was evaluated by (MTT) assay. Neuroinflammation was induced in differentiated cell lines by treatment with 3.125 μg/mL of LPS for 12 h. Upon induction, the cell lines were treated with different concentrations (3.125, 6.25, 12.5, 25, 50, 100 μM) of simvastatin and incubated in a humidified CO2 incubator for 24 to 48 h. The optimum concentrations of LPS and simvastatin were found to be 3.125 μg/mL and 25 μM, respectively, with a cell viability of more than 90% at 24 h postincubation. Furthermore, proinflammatory marker expression was analyzed by flow cytometry and showed a decrease in interferon-γ, interleukin 6, nuclear factor-κB p65, and tumor necrosis factor-α in simvastatin-treated and LPS-induced neuroinflammatory cells, and the mean fluorescent values were found to be 21.75 ± 0.76, 20.9 ± 1.90, 19.72 ± 1.29, and 16.82 ± 0.97, respectively, as compared to the untreated cells. Thus, we show that simvastatin has the potential to regulate the anti-inflammatory response in microglial cells upon LPS challenge. Hence, simvastatin can be employed as a potent anti-inflammatory drug against neuroinflammatory diseases and neurodegenerative disorders.
    MeSH terms: Animals; Anti-Inflammatory Agents; Carbon Dioxide; Cell Line; Cell Survival; Flow Cytometry; T-Lymphocytes, Helper-Inducer; Interferon-gamma; Lipopolysaccharides; Tumor Necrosis Factor-alpha; Interleukin-6; Cytokines; NF-kappa B; Microglia; Neurodegenerative Diseases; Simvastatin; Rats
  5. Mosaheb MUFZ, Khan NA, Siddiqui R
    Iran J Basic Med Sci, 2018 Sep;21(9):873-877.
    PMID: 30524685 DOI: 10.22038/IJBMS.2018.30442.7339
    OBJECTIVES: To present a brief overview of various natural sources of antimicrobials with the aim of highlighting invertebrates living in polluted environments as additional sources of antimicrobials.

    MATERIALS AND METHODS: A PubMed search using antibacterials, antimicrobials, invertebrates, and natural products as keywords was carried out. In addition, we consulted conference proceedings, original unpublished research undertaken in our laboratories, and discussions in specific forums.

    RESULTS: Representative of a stupefying 95% of the fauna, invertebrates are fascinating organisms which have evolved strategies to survive germ-infested environments, yet they have largely been ignored. Since invertebrates such as cockroaches inhabit hazardous environments which are rampant with pathogens, they must have developed defense mechanisms to circumvent infections. This is corroborated by the presence of antimicrobial molecules in the nervous systems and hemolymph of cockroaches. Antimicrobial compounds have also been unraveled from the nervous, adipose, and salivary glandular tissues of locusts. Interestingly, the venoms of arthropods including ants, scorpions, and spiders harbor toxins, but also possess multiple antimicrobials.

    CONCLUSION: These findings have rekindled the hopes for newer and enhanced therapeutic agents derived from a plentiful and diverse resource to combat fatal infectious diseases. Such antimicrobials from unusual sources can potentially be translated into clinical practice, however intensive research is needed over the next several years to realize these expectations.

  6. Ibrahim M, Mikail MA, Ahmed IA, Abdul Ghani R
    J Nutr Metab, 2018;2018:8406193.
    PMID: 30524759 DOI: 10.1155/2018/8406193
    Purpose: Cardiovascular disease (CVD) is the leading and the most critical type of chronic disease. Atherosclerosis is the most common cause of CVD. Inflammation has been progressively acknowledged as a vital and central player in the pathophysiology of atherosclerosis. Baccaurea angulata is an underutilized fruit of the island of Borneo. It was obtained from Bau, Sarawak, Malaysia. In our previous studies, B. angulata did not only increase antioxidant enzyme activities, but also slowed the lipid peroxidation process in high-cholesterol-fed rabbits. It was hypothesized that B. angulata fruit would exert an anti-inflammatory effect. This study, therefore, aimed at evaluating and comparing the effects of three different B. angulata whole fruit (WF) juice doses on 11 serum inflammatory biomarkers of atherosclerosis.

    Methods: Thirty-five male New Zealand white rabbits were divided into seven groups (n=5). Group CH was fed 1% cholesterol diet only, group C1 was fed 1% cholesterol diet and 0.5 ml/kg/day B. angulata WF juice, group C2 was fed 1% cholesterol diet and 1.0 ml/kg/day B. angulata WF juice, group C3 was fed 1% cholesterol diet and 1.5 ml/kg/day B. angulata WF juice, group N was fed standard pellet only, group N1 was fed standard pellet and 0.5 ml/kg/day B. angulata WF juice, and group N2 was fed standard pellet and 1.0 ml/kg/day B. angulata WF juice for 12 weeks.

    Results: The administration of the various juices reduced the concentrations of induced serum inflammatory biomarkers.

    Conclusion: This protective effect of B. angulata fruit against cardiovascular risk might be due to its polyphenol content.

  7. Palihakkara CR, Dassanayake S, Jayawardena C, Senanayake IP
    J Health Pollut, 2018 Mar;8(17):14-19.
    PMID: 30524845 DOI: 10.5696/2156-9614-8.17.14
    Background: Acid mine drainage (AMD) is a major environmental impact associated with the mining industry. Elevated acidic conditions resulting from the discharge of AMD into the surrounding environment can cause heavy metals to dissolve and transport through water streams and accumulate in the aquatic environment, posing a risk to the health of living organisms. There have been several novel approaches in the remediation of AMD involving passive treatment techniques. The constructed treatment wetland approach is a passive remediation option that has proven to be a cost effective and long-lasting solution in abating toxic pollutant concentrations.

    Objectives: The present study investigates the applicability of water hyacinth (Eichhornia crassipes), a tropical aquatic plant with reported heavy metal hyper-accumulation in microcosm floating wetland treatment systems designed to remediate AMD with copper (Cu) and cadmium (Cd) concentrations exceeding threshold limits.

    Methods: Twelve water hyacinth samples were prepared with varying concentrations of Cu (1 mg/L, 2 mg/L, 4 mg/L) and Cd (0.005 mg/L, 0.01 mg/L, 0.02 mg/L). Water samples of 5 ml each were collected from each sample at 24-hour intervals for analysis with an atomic absorption spectrometer.

    Results: Plant growth varied according to Cu and Cd concentrations and no plants survived for more than 14 days. There was a significant discrepancy in the rate at which the Cd concentrations abated. The rate of reduction was rapid for higher concentrations and after 24 hours a substantial reduction was achieved. There was a reduction in Cu concentration after the first 24-hour period, and after the next 24-hour period the concentrations were again elevated in the samples at initial concentrations of 2 mg/L and A4 mg/L. 4 mg/L Cu concentration was shown to be toxic to the plants, as they had low accumulations and rapid dying was evident.

    Conclusions: Water hyacinth has the capability to reduce both Cu and Cd concentrations, except at an initial concentration of 4 mg/L of Cu, which was toxic to the plants.

    Competing Interests: The authors declare no competing financial interests.

    MeSH terms: Cadmium; Copper; Mining; Spectrophotometry, Atomic; Water; Metals, Heavy; Hyacinthus; Eichhornia; Rivers; Wetlands; Plant Development
  8. Danjuma L, Mok PL, Higuchi A, Hamat RA, Teh SW, Koh AE, et al.
    Regen Ther, 2018 Dec;9:100-110.
    PMID: 30525080 DOI: 10.1016/j.reth.2018.09.001
    INTRODUCTION: Anti-tuberculosis agent rifampicin is extensively used for its effectiveness. Possible complications of tuberculosis and prolonged rifampicin treatment include kidney damage; these conditions can lead to reduced efficiency of the affected kidney and consequently to other diseases. Bone marrow-derived mesenchymal stem cells (BMMSCs) can be used in conjunction with rifampicin to avert kidney damage; because of its regenerative and differentiating potentials into kidney cells. This research was designed to assess the modulatory and regenerative potentials of MSCs in averting kidney damage due to rifampicin-induced kidney toxicity in Wistar rats and their progenies. BMMSCs used in this research were characterized according to the guidelines of International Society for Cellular Therapy.

    METHODS: The rats (male and female) were divided into three experimental groups, as follows: Group 1: control rats (4 males & 4 females); Group 2: rats treated with rifampicin only (4 males & 4 females); and Group 3: rats treated with rifampicin plus MSCs (4 males & 4 females). Therapeutic doses of rifampicin (9 mg/kg/day for 3-months) and MSCs infusions (twice/month for 3-months) were administered orally and intravenously respectively. At the end of the three months, the animals were bred together to determine if the effects would carry over to the next generation. Following breeding, the rats were sacrificed to harvest serum for biochemical analysis and the kidneys were also harvested for histological analysis and quantification of the glomeruli size, for the adult rats and their progenies.

    RESULTS: The results showed some level of alterations in the biochemical indicators and histopathological damage in the rats that received rifampicin treatment alone, while the control and stem cells treated group showed apparently normal to nearly normal levels of both bio-indicators and normal histological architecture.

    CONCLUSIONS: Intravenous administration of MSCs yielded sensible development, as seen from biochemical indicators, histology and the quantitative cell analysis, hence implying the modulatory and regenerative properties of MSCs.

  9. Shiraku H, Nakashima M, Takeshita S, Khoo CS, Haniffa M, Ch'ng GS, et al.
    Epilepsia Open, 2018 Dec;3(4):495-502.
    PMID: 30525118 DOI: 10.1002/epi4.12272
    Objective: Vitamin B6-dependent epilepsies are treatable disorders caused by variants in several genes, such as ALDH7A1,PNPO, and others. Recently, biallelic variants in PLPBP, formerly known as PROSC, were identified as a novel cause of vitamin B6-dependent epilepsies. Our objective was to further delineate the phenotype of PLPBP mutation.

    Methods: We identified 4 unrelated patients harboring a total of 4 variants in PLPBP, including 3 novel variants, in a cohort of 700 patients with developmental and epileptic encephalopathies. Clinical information in each case was collected.

    Results: Each patient had a different clinical course of epilepsy, with seizure onset from the first day of life to 3 months of age. Generalized tonic-clonic seizures were commonly noted. Myoclonic seizures or focal seizures were also observed in 2 patients. Interictal electroencephalography showed variable findings, such as suppression burst, focal or multifocal discharges, and diffuse slow activity. Unlike previous reports, all the patients had some degree of intellectual disability, although some of them had received early treatment with vitamin B6, suggesting that different mutation types influence the severity and outcome of the seizures.

    Significance: PLPBP variants should be regarded as among the causative genes of developmental and epileptic encephalopathy, even when it occurs after the neonatal period. Early diagnosis and proper treatment with pyridoxine or pyridoxal phosphate is essential to improve the neurologic prognosis in neonates or young children with poorly controlled seizures.

  10. Lim YP, Yahya N, Izaham A, Kamaruzaman E, Zainuddin MZ, Wan Mat WR, et al.
    Turk J Med Sci, 2018 Dec 12;48(6):1219-1227.
    PMID: 30541250 DOI: 10.3906/sag-1802-126
    Background/aim: Regional anesthesia for surgery is associated with increased anxiety for patients. This study aimed to compare the
    effect of propofol and dexmedetomidine infusion on perioperative anxiety during regional anesthesia.

    Materials and methods: Eighty-four patients were randomly divided into two groups receiving either study drug infusion. Anxiety
    score, level of sedation using the Bispectral Index and Observer’s Assessment of Alertness and Sedation, hemodynamic stability, and
    overall patient’s feedback on anxiolysis were assessed.

    Results: Both groups showed a significant drop in mean anxiety score at 10 and 30 min after starting surgery. Difference in median
    anxiety scores showed a significant reduction in anxiety score at the end of the surgery in the dexmedetomidine group compared to the
    propofol group. Dexmedetomidine and propofol showed a significant drop in mean arterial pressure in the first 30 min and first 10 min
    respectively. Both drugs demonstrated a significant drop in heart rate in the first 20 min from baseline after starting the drug infusion.
    Patients in the dexmedetomidine group (76.20%) expressed statistically excellent feedback on anxiolysis compared to patients in the
    propofol group (45.20%).

    Conclusion: Dexmedetomidine infusion was found to significantly reduce anxiety levels at the end of surgery compared to propofol
    during regional anesthesia.

    MeSH terms: Anesthesia, Conduction; Anxiety; Heart Rate; Humans; Propofol; Dexmedetomidine; Arterial Pressure
  11. Nur Husna SM, Tan HT, Mohamud R, Dyhl-Polk A, Wong KK
    Ther Adv Med Oncol, 2018;10:1758835918808509.
    PMID: 30542378 DOI: 10.1177/1758835918808509
    Breast cancer is the global leading cause of cancer-related death in women and it represents a major health burden worldwide. One of the promising breast cancer therapeutic avenues is through small molecule inhibitors (SMIs) which have undergone rapid progress with successful clinical trials. Recently, three emerging and vital groups of proteins are targeted by SMIs for breast cancer treatment, namely cyclin-dependent kinase 4 and 6 (CDK4/6), poly (adenosine diphosphate-ribose) polymerase (PARP) and phosphoinositide 3-kinase (PI3K). Several of these inhibitors have been approved for the treatment of breast cancer patients or progressed into late-stage clinical trials. Thus, modeling from these successful clinical trials, as well as their limitations, is pivotal for future development and trials of other inhibitors or therapeutic regimens targeting breast cancer patients. In this review, we discuss eight recently approved or novel SMIs against CDK4/6 (palbociclib, ribociclib and abemaciclib), PARP (olaparib, veliparib and talazoparib), and PI3K (buparlisib and alpelisib). The mechanisms of action, series of clinical trials and limitations are described for each inhibitor.
    MeSH terms: Adenosine Diphosphate; Aminopyridines; Benzimidazoles; Breast Neoplasms; Female; Humans; Morpholines; Phthalazines; Piperazines; Purines; Pyridines; Ribose; Phosphatidylinositol 3-Kinases; Cyclin-Dependent Kinase 4
  12. Krishnan P, Lee FK, Chong KW, Mai CW, Muhamad A, Lim SH, et al.
    Org. Lett., 2018 12 21;20(24):8014-8018.
    PMID: 30543301 DOI: 10.1021/acs.orglett.8b03592
    Two new monoterpenoid indole alkaloids, alstoscholactine (1) and alstolaxepine (2), were isolated from Alstonia scholaris. Compound 1 represents a rearranged stemmadenine alkaloid with an unprecedented C-6-C-19 connectivity, whereas compound 2 represents a 6,7- seco-angustilobine B-type alkaloid incorporating a rare γ-lactone-bridged oxepane ring system. Their structures and absolute configurations were determined by spectroscopic analyses. Compound 1 was successfully semisynthesized from 19 E-vallesamine. Compound 2 induced marked vasorelaxation in rat isolated aortic rings precontracted with phenylephrine.
    MeSH terms: Animals; Aorta/drug effects; Cycloheptanes/isolation & purification; Cycloheptanes/pharmacology*; Cycloheptanes/chemistry; Dose-Response Relationship, Drug; Heterocyclic Compounds with 4 or More Rings/isolation & purification; Heterocyclic Compounds with 4 or More Rings/pharmacology*; Heterocyclic Compounds with 4 or More Rings/chemistry; Humans; Indoles/isolation & purification; Indoles/pharmacology*; Indoles/chemistry; Lactones/isolation & purification; Lactones/pharmacology*; Lactones/chemistry; Male; Models, Molecular; Molecular Conformation; Oxepins/isolation & purification; Oxepins/pharmacology*; Oxepins/chemistry; Structure-Activity Relationship; Crystallography, X-Ray; Alstonia/chemistry*; Cell Line, Tumor; Secologanin Tryptamine Alkaloids/isolation & purification; Secologanin Tryptamine Alkaloids/pharmacology*; Secologanin Tryptamine Alkaloids/chemistry; Rats
  13. Tallman DA, Sahathevan S, Karupaiah T, Khosla P
    Nutrients, 2018 Dec 07;10(12).
    PMID: 30544535 DOI: 10.3390/nu10121945
    Patients with chronic kidney disease (CKD) are often instructed to adhere to a renal-specific diet depending on the severity and stage of their kidney disease. The prescribed diet may limit certain nutrients, such as phosphorus and potassium, or encourage the consumption of others, such as high biological value (HBV) proteins. Eggs are an inexpensive, easily available and high-quality source of protein, as well as a rich source of leucine, an essential amino acid that plays a role in muscle protein synthesis. However, egg yolk is a concentrated source of both phosphorus and the trimethylamine N-oxide precursor, choline, both of which may have potentially harmful effects in CKD. The yolk is also an abundant source of cholesterol which has been extensively studied for its effects on lipoprotein cholesterol and the risk of cardiovascular disease. Efforts to reduce dietary cholesterol to manage dyslipidemia in dialysis patients (already following a renal diet) have not been shown to offer additional benefit. There is a paucity of data regarding the impact of egg consumption on lipid profiles of CKD patients. Additionally, egg consumption has not been associated with the risk of developing CKD based on epidemiological studies. The egg yolk also contains bioactive compounds, including lutein, zeaxanthin, and vitamin D, which may confer health benefits in CKD patients. Here we review research on egg intake and CKD, discuss both potential contraindications and favorable effects of egg consumption, and describe the need for further research examining egg intake and outcomes in the CKD and end-stage renal disease population.
    MeSH terms: Diet/statistics & numerical data*; Eggs*; Humans; Middle Aged; Nutritive Value; Renal Insufficiency, Chronic/diet therapy*; Renal Insufficiency, Chronic/epidemiology*
  14. Talib NAA, Salam F, Sulaiman Y
    Sensors (Basel), 2018 Dec 07;18(12).
    PMID: 30544568 DOI: 10.3390/s18124324
    Clenbuterol (CLB) is an antibiotic and illegal growth promoter drug that has a long half-life and easily remains as residue and contaminates the animal-based food product that leads to various health problems. In this work, electrochemical immunosensor based on poly(3,4-ethylenedioxythiophene)/graphene oxide (PEDOT/GO) modified screen-printed carbon electrode (SPCE) for CLB detection was developed for antibiotic monitoring in a food product. The modification of SPCE with PEDOT/GO as a sensor platform was performed through electropolymerization, while the electrochemical assay was accomplished while using direct competitive format in which the free CLB and clenbuterol-horseradish peroxidase (CLB-HRP) in the solution will compete to form binding with the polyclonal anti-clenbuterol antibody (Ab) immobilized onto the modified electrode surface. A linear standard CLB calibration curve with R² = 0.9619 and low limit of detection (0.196 ng mL-1) was reported. Analysis of milk samples indicated that this immunosensor was able to detect CLB in real samples and the results that were obtained were comparable with enzyme-linked immunosorbent assays (ELISA).
    MeSH terms: Animals; Animal Feed/analysis; Carbon/chemistry; Clenbuterol/isolation & purification*; Clenbuterol/toxicity; Electrodes; Food Analysis/methods*; Gold/chemistry; Graphite/chemistry*; Horseradish Peroxidase/chemistry; Humans; Polymers/chemistry; Biosensing Techniques/methods*; Bicyclo Compounds, Heterocyclic/chemistry; Electrochemical Techniques/methods; Limit of Detection
  15. Mohamad MH, Sali A, Hashim F, Nordin R, Takyu O
    Sensors (Basel), 2018 Dec 10;18(12).
    PMID: 30544655 DOI: 10.3390/s18124351
    This paper investigated the throughput performance of a secondary user (SU) for a random primary user (PU) activity in a realistic experimental model. This paper proposed a sensing and frame duration of the SU to maximize the SU throughput under the collision probability constraint. The throughput of the SU and the probability of collisions depend on the pattern of PU activities. The pattern of PU activity was obtained and modelled from the experimental data that measure the wireless local area network (WLAN) environment. The WLAN signal has detected the transmission opportunity length (TOL) which was analyzed and clustered into large and small durations in the CTOL model. The performance of the SU is then analyzed and compared with static and dynamic PU models. The results showed that the SU throughput in the CTOL model was higher than the static and dynamic models by almost 45% and 12.2% respectively. Furthermore, the probability of collisions in the network and the SU throughput were influenced by the value of the minimum contention window and the maximum back-off stage. The simulation results revealed that the higher contention window had worsened the SU throughput even though the channel has a higher number of TOLs.
    MeSH terms: Environment; Local Area Networks; Models, Theoretical; Probability
  16. Ismail A, Idris MYI, Ayub MN, Por LY
    Sensors (Basel), 2018 Dec 10;18(12).
    PMID: 30544660 DOI: 10.3390/s18124353
    Smart manufacturing enables an efficient manufacturing process by optimizing production and product transaction. The optimization is performed through data analytics that requires reliable and informative data as input. Therefore, in this paper, an accurate data capture approach based on a vision sensor is proposed. Three image recognition methods are studied to determine the best vision-based classification technique, namely Bag of Words (BOW), Spatial Pyramid Matching (SPM) and Convolutional Neural Network (CNN). The vision-based classifiers categorize the apple as defective and non-defective that can be used for automatic inspection, sorting and further analytics. A total of 550 apple images are collected to test the classifiers. The images consist of 275 non-defective and 275 defective apples. The defective category includes various types of defect and severity. The vision-based classifiers are trained and evaluated according to the K-fold cross-validation. The performances of the classifiers from 2-fold, 3-fold, 4-fold, 5-fold and 10-fold are compared. From the evaluation, SPM with SVM classifier attained 98.15% classification accuracy for 10-fold and outperformed the others. In terms of computational time, CNN with SVM classifier is the fastest. However, minimal time difference is observed between the computational time of CNN and SPM, which were separated by only 0.05 s.
    MeSH terms: Data Accuracy; Food Additives; Research Design; Neural Networks (Computer); Malus
  17. Al-Mqdashi A, Sali A, Noordin NK, Hashim SJ, Nordin R
    Sensors (Basel), 2018 Dec 10;18(12).
    PMID: 30544684 DOI: 10.3390/s18124360
    Channel rendezvous is an initial and important process for establishing communications between secondary users (SUs) in distributed cognitive radio networks. Due to the drawbacks of the common control channel (CCC) based rendezvous approach, channel hopping (CH) has attracted a lot of research interests for achieving blind rendezvous. To ensure rendezvous within a finite time, most of the existing CH-based rendezvous schemes generate their CH sequences based on the whole global channel set in the network. However, due to the spatial and temporal variations in channel availabilities as well as the limitation of SUs sensing capabilities, the local available channel set (ACS) for each SU is usually a small subset of the global set. Therefore, following these global-based generated CH sequences can result in extensively long time-to-rendezvous (TTR) especially when the number of unavailable channels is large. In this paper, we propose two matrix-based CH rendezvous schemes in which the CH sequences are generated based on the ACSs only. We prove the guaranteed and full diversity rendezvous of the proposed schemes by deriving the theoretical upper bounds of their maximum TTRs. Furthermore, extensive simulation comparisons with other existing works are conducted which illustrate the superior performance of our schemes in terms of the TTR metrics.
    MeSH terms: Cognition; Communication; Movement; Research
  18. Abdullah N, Murad NAA, Attia J, Oldmeadow C, Kamaruddin MA, Jalal NA, et al.
    Int J Environ Res Public Health, 2018 Dec 10;15(12).
    PMID: 30544761 DOI: 10.3390/ijerph15122813
    The prevalence of type 2 diabetes is escalating rapidly in Asian countries, with the rapid increase likely attributable to a combination of genetic and lifestyle factors. Recent research suggests that common genetic risk variants contribute minimally to the rapidly rising prevalence. Rather, recent changes in dietary patterns and physical activity may be more important. This nested case-control study assessed the association and predictive utility of type 2 diabetes lifestyle risk factors in participants from Malaysia, an understudied Asian population with comparatively high disease prevalence. The study sample comprised 4077 participants from The Malaysian Cohort project and included sub-samples from the three major ancestral groups: Malay (n = 1323), Chinese (n = 1344) and Indian (n = 1410). Association of lifestyle factors with type 2 diabetes was assessed within and across ancestral groups using logistic regression. Predictive utility was quantified and compared between groups using the Area Under the Receiver-Operating Characteristic Curve (AUC). In predictive models including age, gender, waist-to-hip ratio, physical activity, location, family history of diabetes and average sleep duration, the AUC ranged from 0.76 to 0.85 across groups and was significantly higher in Chinese than Malays or Indians, likely reflecting anthropometric differences. This study suggests that obesity, advancing age, a family history of diabetes and living in a rural area are important drivers of the escalating prevalence of type 2 diabetes in Malaysia.
    MeSH terms: Adult; Aged; Diabetes Mellitus, Type 2/etiology; Diabetes Mellitus, Type 2/epidemiology*; Ethnic Groups/statistics & numerical data; Female; Humans; Life Style*; Malaysia/epidemiology; Male; Middle Aged; Prospective Studies; Risk Factors; Prevalence; Case-Control Studies; Area Under Curve
  19. Alhasa KM, Mohd Nadzir MS, Olalekan P, Latif MT, Yusup Y, Iqbal Faruque MR, et al.
    Sensors (Basel), 2018 Dec 11;18(12).
    PMID: 30544953 DOI: 10.3390/s18124380
    Conventional air quality monitoring systems, such as gas analysers, are commonly used in many developed and developing countries to monitor air quality. However, these techniques have high costs associated with both installation and maintenance. One possible solution to complement these techniques is the application of low-cost air quality sensors (LAQSs), which have the potential to give higher spatial and temporal data of gas pollutants with high precision and accuracy. In this paper, we present DiracSense, a custom-made LAQS that monitors the gas pollutants ozone (O₃), nitrogen dioxide (NO₂), and carbon monoxide (CO). The aim of this study is to investigate its performance based on laboratory calibration and field experiments. Several model calibrations were developed to improve the accuracy and performance of the LAQS. Laboratory calibrations were carried out to determine the zero offset and sensitivities of each sensor. The results showed that the sensor performed with a highly linear correlation with the reference instrument with a response-time range from 0.5 to 1.7 min. The performance of several calibration models including a calibrated simple equation and supervised learning algorithms (adaptive neuro-fuzzy inference system or ANFIS and the multilayer feed-forward perceptron or MLP) were compared. The field calibration focused on O₃ measurements due to the lack of a reference instrument for CO and NO₂. Combinations of inputs were evaluated during the development of the supervised learning algorithm. The validation results demonstrated that the ANFIS model with four inputs (WE OX, AE OX, T, and NO₂) had the lowest error in terms of statistical performance and the highest correlation coefficients with respect to the reference instrument (0.8 < r < 0.95). These results suggest that the ANFIS model is promising as a calibration tool since it has the capability to improve the accuracy and performance of the low-cost electrochemical sensor.
    MeSH terms: Supervised Machine Learning; Air Pollution; Algorithms; Calibration; Carbon Monoxide; Developing Countries; Environmental Pollutants; Maintenance; Nitrogen Dioxide; Ozone
  20. Elmqvist T, Siri J, Andersson E, Anderson P, Bai X, Das PK, et al.
    Sustain Sci, 2018;13(6):1549-1564.
    PMID: 30546487 DOI: 10.1007/s11625-018-0611-0
    Cities are currently experiencing serious, multifaceted impacts from global environmental change, especially climate change, and the degree to which they will need to cope with and adapt to such challenges will continue to increase. A complex systems approach inspired by evolutionary theory can inform strategies for policies and interventions to deal with growing urban vulnerabilities. Such an approach would guide the design of new (and redesign of existing) urban structures, while promoting innovative integration of grey, green and blue infrastructure in service of environmental and health objectives. Moreover, it would contribute to more flexible, effective policies for urban management and the use of urban space. Four decades ago, in a seminal paper in Science, the French evolutionary biologist and philosopher Francois Jacob noted that evolution differs significantly in its characteristic modes of action from processes that are designed and engineered de novo (Jacob in Science 196(4295):1161-1166, 1977). He labeled the evolutionary process "tinkering", recognizing its foundation in the modification and molding of existing traits and forms, with occasional dramatic shifts in function in the context of changing conditions. This contrasts greatly with conventional engineering and design approaches that apply tailor-made materials and tools to achieve well-defined functions that are specified a priori. We here propose that urban tinkering is the application of evolutionary thinking to urban design, engineering, ecological restoration, management and governance. We define urban tinkering as:A mode of operation, encompassing policy, planning and management processes, that seeks to transform the use of existing and design of new urban systems in ways that diversify their functions, anticipate new uses and enhance adaptability, to better meet the social, economic and ecological needs of cities under conditions of deep uncertainty about the future.This approach has the potential to substantially complement and augment conventional urban development, replacing predictability, linearity and monofunctional design with anticipation of uncertainty and non-linearity and design for multiple, potentially shifting functions. Urban tinkering can function by promoting a diversity of small-scale urban experiments that, in aggregate, lead to large-scale often playful innovative solutions to the problems of sustainable development. Moreover, the tinkering approach is naturally suited to exploring multi-functional uses and approaches (e.g., bricolage) for new and existing urban structures and policies through collaborative engagement and analysis. It is thus well worth exploring as a means of delivering co-benefits for environment and human health and wellbeing. Indeed, urban tinkering has close ties to systems approaches, which often are recognized as critical to sustainable development. We believe this concept can help forge much-closer, much-needed ties among engineers, architects, evolutionary ecologists, health specialists, and numerous other urban stakeholders in developing innovative, widely beneficial solutions for society and contribute to successful implementation of SDG11 and the New Urban Agenda.
    MeSH terms: Cities; Conservation of Natural Resources; Ecology; Government; Humans; Specialization; Systems Analysis; Urban Renewal; Uncertainty; Climate Change
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