Displaying publications 1 - 20 of 403 in total

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  1. Zubair M, Abdullah MZ, Ahmad KA
    Comput Math Methods Med, 2013;2013:727362.
    PMID: 23983811 DOI: 10.1155/2013/727362
    The accuracy of the numerical result is closely related to mesh density as well as its distribution. Mesh plays a very significant role in the outcome of numerical simulation. Many nasal airflow studies have employed unstructured mesh and more recently hybrid mesh scheme has been utilized considering the complexity of anatomical architecture. The objective of this study is to compare the results of hybrid mesh with unstructured mesh and study its effect on the flow parameters inside the nasal cavity. A three-dimensional nasal cavity model is reconstructed based on computed tomographic images of a healthy Malaysian adult nose. Navier-Stokes equation for steady airflow is solved numerically to examine inspiratory nasal flow. The pressure drop obtained using the unstructured computational grid is about 22.6 Pa for a flow rate of 20 L/min, whereas the hybrid mesh resulted in 17.8 Pa for the same flow rate. The maximum velocity obtained at the nasal valve using unstructured grid is 4.18 m/s and that with hybrid mesh is around 4.76 m/s. Hybrid mesh reported lower grid convergence index (GCI) than the unstructured mesh. Significant differences between unstructured mesh and hybrid mesh are determined highlighting the usefulness of hybrid mesh for nasal airflow studies.
    Matched MeSH terms: Models, Biological
  2. Zouache MA, Eames I, Samsudin A
    PLoS One, 2016;11(3):e0151490.
    PMID: 26990431 DOI: 10.1371/journal.pone.0151490
    In vertebrates, intraocular pressure (IOP) is required to maintain the eye into a shape allowing it to function as an optical instrument. It is sustained by the balance between the production of aqueous humour by the ciliary body and the resistance to its outflow from the eye. Dysregulation of the IOP is often pathological to vision. High IOP may lead to glaucoma, which is in man the second most prevalent cause of blindness. Here, we examine the importance of the IOP and rate of formation of aqueous humour in the development of vertebrate eyes by performing allometric and scaling analyses of the forces acting on the eye during head movement and the energy demands of the cornea, and testing the predictions of the models against a list of measurements in vertebrates collated through a systematic review. We show that the IOP has a weak dependence on body mass, and that in order to maintain the focal length of the eye, it needs to be an order of magnitude greater than the pressure drop across the eye resulting from gravity or head movement. This constitutes an evolutionary constraint that is common to all vertebrates. In animals with cornea-based optics, this constraint also represents a condition to maintain visual acuity. Estimated IOPs were found to increase with the evolution of terrestrial animals. The rate of formation of aqueous humour was found to be adjusted to the metabolic requirements of the cornea, scaling as Vac(0.67), where Vac is the volume of the anterior chamber. The present work highlights an interdependence between IOP and aqueous flow rate crucial to ocular function that must be considered to understand the evolution of the dioptric apparatus. It should also be taken into consideration in the prevention and treatment of glaucoma.
    Matched MeSH terms: Models, Biological*
  3. Zeng H, Zhang J, Preising GA, Rubel T, Singh P, Ritz A
    Nucleic Acids Res, 2021 07 02;49(W1):W257-W262.
    PMID: 34037782 DOI: 10.1093/nar/gkab420
    Networks have been an excellent framework for modeling complex biological information, but the methodological details of network-based tools are often described for a technical audience. We have developed Graphery, an interactive tutorial webserver that illustrates foundational graph concepts frequently used in network-based methods. Each tutorial describes a graph concept along with executable Python code that can be interactively run on a graph. Users navigate each tutorial using their choice of real-world biological networks that highlight the diverse applications of network algorithms. Graphery also allows users to modify the code within each tutorial or write new programs, which all can be executed without requiring an account. Graphery accepts ideas for new tutorials and datasets that will be shaped by both computational and biological researchers, growing into a community-contributed learning platform. Graphery is available at https://graphery.reedcompbio.org/.
    Matched MeSH terms: Models, Biological*
  4. Zakaria Z, Badhan RKS
    Eur J Pharm Sci, 2018 Jul 01;119:90-101.
    PMID: 29635009 DOI: 10.1016/j.ejps.2018.04.012
    Lumefantrine is a widely used antimalarial in children in sub-Saharan Africa and is predominantly metabolised by CYP3A4. The concomitant use of lumefantrine with the antiretroviral efavirenz, which is metabolised by CYP2B6 and is an inducer of CYP3A4, increases the risk of lumefantrine failure and can result in an increased recrudescence rate in HIV-infected children. This is further confounded by CYP2B6 being highly polymorphic resulting in a 2-3 fold higher efavirenz plasma concentration in polymorphic subjects, which enhances the potential for an efavirenz-lumefantrine drug-drug interaction (DDI). This study developed a population-based PBPK model capable of predicting the impact of efavirenz-mediated DDIs on lumefantrine pharmacokinetics in African paediatric population groups, which also considered the polymorphic nature of CYP2B6. The validated model demonstrated a significant difference in lumefantrine target day 7 concentrations (Cd7) in the presence and absence of efavirenz and confirmed the capability of efavirenz to initiate this DDI. This was more apparent in the *6/*6 compared to *1/*1 population group and resulted in a significantly lower (P 
    Matched MeSH terms: Models, Biological
  5. Zakaria MR, Hirata S, Hassan MA
    Bioresour Technol, 2015 Jan;176:142-8.
    PMID: 25460995 DOI: 10.1016/j.biortech.2014.11.027
    The present works investigate hydrothermal pretreatment of oil palm empty fruit bunch and oil palm frond fiber in a batch tube reactor system with temperature and time range from 170 to 250°C and 10 to 20min, respectively. The behavior of soluble sugars, acids, furans, and phenols dramatically changed over treatment severities as determined by HPLC. The cellulose-rich treated solids were analyzed by SEM, WAXD, and BET surface area. Enzymatic hydrolysis was performed from both pretreated slurries and washed solid, and data obtained suggested that tannic acid derived from lignin degradation was a potential cellulase inhibitor. Both partial removal of hemicellulose and migration of lignin during hydrothermal pretreatment caused structural changes on the cellulose-hemicellulose-lignin matrix, resulting in the opening and expansion of specific surface area and pore volume. The current results provided important factors that maximize conversion of cellulose to glucose from oil palm biomass by hydrothermal process.
    Matched MeSH terms: Models, Biological
  6. Zainal Z, Longman AJ, Hurst S, Duggan K, Hughes CE, Caterson B, et al.
    Lipids, 2009 Jul;44(7):581-92.
    PMID: 19449050 DOI: 10.1007/s11745-009-3304-8
    Palm oil is one of the most important edible oils in the world. Its composition (rich in palmitate and oleate) make it suitable for general food uses but its utility could be increased if its fatty acid quality could be varied. In this study, we have modified a palm olein fraction by transesterification with the n-3 polyunsaturated fatty acids, alpha-linolenate or eicosapentaenoic acid (EPA). Evaluation of the potential nutritional efficacy of the oils was made using chondrocyte culture systems which can be used to mimic many of the degenerative and inflammatory pathways involved in arthritis. On stimulation of such cultures with interleukin-1alpha, they showed increased expression of cyclooxygenase-2, the inflammatory cytokines tumour necrosis factor-alpha (TNF-alpha), IL-1alpha and IL-1beta and the proteinase ADAMTS-4. This increased expression was not affected by challenge of the cultures with palm olein alone but showed concentration-dependent reduction by the modified oil in a manner similar to EPA. These results show clearly that it is possible to modify palm oil conveniently to produce a nutraceutical with effective anti-inflammatory properties.
    Matched MeSH terms: Models, Biological
  7. Yusoff N, Abu Osman NA, Pingguan-Murphy B
    Med Eng Phys, 2011 Jul;33(6):782-8.
    PMID: 21356602 DOI: 10.1016/j.medengphy.2011.01.013
    A mechanical-conditioning bioreactor has been developed to provide bi-axial loading to three-dimensional (3D) tissue constructs within a highly controlled environment. The computer-controlled bioreactor is capable of applying axial compressive and shear deformations, individually or simultaneously at various regimes of strain and frequency. The reliability and reproducibility of the system were verified through validation of the spatial and temporal accuracy of platen movement, which was maintained over the operating length of the system. In the presence of actual specimens, the system was verified to be able to deliver precise bi-axial load to the specimens, in which the deformation of every specimen was observed to be relatively homogeneous. The primary use of the bioreactor is in the culture of chondrocytes seeded within an agarose hydrogel while subjected to physiological compressive and shear deformation. The system has been designed specifically to permit the repeatable quantification and characterisation of the biosynthetic activity of cells in response to a wide range of short and long term multi-dimensional loading regimes.
    Matched MeSH terms: Models, Biological
  8. Yusof WN, Nagaratnam M, Koh CL, Puthucheary S, Pang T
    Microbiol. Immunol., 1993;37(8):667-70.
    PMID: 8246829
    Human mononuclear cells pre-labeled with [3H]arachidonic acid were shown to release metabolites following in vitro addition of heat-killed Salmonella typhi (HKST). The amount of label released was significantly higher than that seen with live S. typhi (LST). Addition of increasing amounts of HKST resulted in an increased release of metabolites. Enzyme immunoassay of the culture supernatants revealed that the bulk of the metabolite released was prostaglandin E2 (PGE2). Leukotriene B4 (LTB4) and leukotriene C4 (LTC4) were not detectable in the culture supernatants. The significance and implications of these results are discussed.
    Matched MeSH terms: Models, Biological
  9. Yusof SR, Abbott NJ, Avdeef A
    Eur J Pharm Sci, 2017 Aug 30;106:274-286.
    PMID: 28614733 DOI: 10.1016/j.ejps.2017.06.016
    Most studies of blood-brain barrier (BBB) permeability and transport are conducted at a single pH, but more detailed information can be revealed by using multiple pH values. A pH-dependent biophysical model was applied to the mechanistic analysis of published pH-dependent BBB luminal uptake data from three opioid derivatives in rat: pentazocine (Suzuki et al., 2002a, 2002b), naloxone (Suzuki et al., 2010a), and oxycodone (Okura et al., 2008). Two types of data were processed: in situ brain perfusion (ISBP) and brain uptake index (BUI). The published perfusion data were converted to apparent luminal permeability values, Papp, and analyzed by the pCEL-X program (Yusof et al., 2014), using the pH-dependent Crone-Renkin equation (pH-CRE) to determine the impact of cerebrovascular flow on the Michaelis-Menten transport parameters (Avdeef and Sun, 2011). For oxycodone, the ISBP data had been measured at pH7.4 and 8.4. The present analysis indicates a 7-fold lower value of the cerebrovascular flow velocity, Fpf, than that expected in the original study. From the pyrilamine-inhibited data, the flow-corrected passive intrinsic permeability value was determined to be P0=398×10-6cm·s-1. The uptake data indicate that the neutral form of oxycodone is affected by a transporter at pH8.4. The extent of the cation uptake was less certain from the available data. For pentazocine, the brain uptake by the BUI method had been measured at pH5.5, 6.5, and 7.4, in a concentration range 0.1-40mM. Under similar conditions, ISBP data were also available. The pH-CRE determined values of Fpf from both methods were nearly the same, and were smaller than the expected value in the original publication. The transport of the cationic pentazocine was not fully saturated at pH5.5 at 40mM. The transport of the neutral species at pH7.4 appeared to reach saturation at 40mM pentazocine concentration, but not at 12mM. In the case of naloxone, a pH-dependent Michaelis-Menten equation (pH-MME) analysis of the data indicated a smooth sigmoidal transition from a higher capacity uptake process affecting cationic naloxone (pH5.0-7.0) to a lower capacity uptake process affecting the neutral drug (pH8.0-8.5), with cross-over point near pH7.4. Evidently, measurements at multiple pH values can reveal important information about both cerebrovascular flow and BBB transport kinetics.
    Matched MeSH terms: Models, Biological
  10. Yin LK, Rajeswari M
    Biomed Mater Eng, 2014;24(6):3333-41.
    PMID: 25227043 DOI: 10.3233/BME-141156
    To segment an image using the random walks algorithm; users are often required to initialize the approximate locations of the objects and background in the image. Due to its segmenting model that is mainly reflected by the relationship among the neighborhood pixels and its boundary conditions, random walks algorithm has made itself sensitive to the inputs of the seeds. Instead of considering the relationship between the neighborhood pixels solely, an attempt has been made to modify the weighting function that accounts for the intensity changes between the neighborhood nodes. Local affiliation within the defined neighborhood region of the two nodes is taken into consideration by incorporating an extra penalty term into the weighting function. Besides that, to better segment images, particularly medical images with texture features, GLCM variance is incorporated into the weighting function through kernel density estimation (KDE). The probability density of each pixel belonging to the initialized seeds is estimated and integrated into the weighting function. To test the performance of the proposed weighting model, several medical images that mainly made up of 174-brain tumor images are experimented. These experiments establish that the proposed method produces better segmentation results than the original random walks.
    Matched MeSH terms: Models, Biological
  11. Yeong CH, Ng KH, Abdullah BJJ, Chung LY, Goh KL, Perkins AC
    Appl Radiat Isot, 2014 Dec;94:216-220.
    PMID: 25222875 DOI: 10.1016/j.apradiso.2014.08.009
    Radionuclide imaging using (111)In, (99m)Tc and (153)Sm is commonly undertaken for the clinical investigation of gastric emptying, intestinal motility and whole gut transit. However the documented evidence concerning internal radiation dosimetry for such studies is not readily available. This communication documents the internal radiation dosimetry for whole gastrointestinal transit studies using (111)In, (99m)Tc and (153)Sm labeled formulations. The findings were compared to the diagnostic reference levels recommended by the United Kingdom Administration of Radioactive Substances Advisory Committee, for gastrointestinal transit studies.
    Matched MeSH terms: Models, Biological*
  12. Yeang HY
    Bioessays, 2009 Nov;31(11):1211-8.
    PMID: 19795408 DOI: 10.1002/bies.200900078
    The plant maintains a 24-h circadian cycle that controls the sequential activation of many physiological and developmental functions. There is empirical evidence suggesting that two types of circadian rhythms exist. Some plant rhythms appear to be set by the light transition at dawn, and are calibrated to circadian (zeitgeber) time, which is measured from sunrise. Other rhythms are set by both dawn and dusk, and are calibrated to solar time that is measured from mid-day. Rhythms on circadian timing shift seasonally in tandem with the timing of dawn that occurs earlier in summer and later in winter. On the other hand, rhythms set to solar time are maintained independently of the season, the timing of noon being constant year-round. Various rhythms that run in-phase and out-of-phase with one another seasonally may provide a means to time and induce seasonal events such as flowering.
    Matched MeSH terms: Models, Biological
  13. Yeang HY
    Ann Bot, 2015 Jul;116(1):15-22.
    PMID: 26070640 DOI: 10.1093/aob/mcv070
    BACKGROUND AND AIMS: An endogenous rhythm synchronized to dawn cannot time photosynthesis-linked genes to peak consistently at noon since the interval between sunrise and noon changes seasonally. In this study, a solar clock model that circumvents this limitation is proposed using two daily timing references synchronized to noon and midnight. Other rhythmic genes that are not directly linked to photosynthesis, and which peak at other times, also find an adaptive advantage in entrainment to the solar rhythm.

    METHODS: Fourteen datasets extracted from three published papers were used in a meta-analysis to examine the cyclic behaviour of the Arabidopsis thaliana photosynthesis-related gene CAB2 and the clock oscillator genes TOC1 and LHY in T cycles and N-H cycles.

    KEY RESULTS: Changes in the rhythms of CAB2, TOC1 and LHY in plants subjected to non-24-h light:dark cycles matched the hypothesized changes in their behaviour as predicted by the solar clock model, thus validating it. The analysis further showed that TOC1 expression peaked ∼5·5 h after mid-day, CAB2 peaked close to noon, while LHY peaked ∼7·5 h after midnight, regardless of the cycle period, the photoperiod or the light:dark period ratio. The solar clock model correctly predicted the zeitgeber timing of these genes under 11 different lighting regimes comprising combinations of seven light periods, nine dark periods, four cycle periods and four light:dark period ratios. In short cycles that terminated before LHY could be expressed, the solar clock correctly predicted zeitgeber timing of its expression in the following cycle.

    CONCLUSIONS: Regulation of gene phases by the solar clock enables the plant to tell the time, by which means a large number of genes are regulated. This facilitates the initiation of gene expression even before the arrival of sunrise, sunset or noon, thus allowing the plant to 'anticipate' dawn, dusk or mid-day respectively, independently of the photoperiod.

    Matched MeSH terms: Models, Biological
  14. Yap MK, Tan NH, Sim SM, Fung SY, Tan CH
    Basic Clin Pharmacol Toxicol, 2015 Oct;117(4):274-9.
    PMID: 25819552 DOI: 10.1111/bcpt.12398
    The treatment protocol of antivenom in snake envenomation remains largely empirical, partly due to the insufficient knowledge of the pharmacokinetics of snake venoms and the effects of antivenoms on the blood venom levels in victims. In this study, we investigated the effect of a polyvalent antivenom on the serum venom antigen levels of Naja sputatrix (Javan spitting cobra) venom in experimentally envenomed rabbits. Intravenous infusion of 4 ml of Neuro Polyvalent Snake Antivenom [NPAV, F(ab')2 ] at 1 hr after envenomation caused a sharp decline of the serum venom antigen levels, followed by transient resurgence an hour later. The venom antigen resurgence was unlikely to be due to the mismatch of pharmacokinetics between the F(ab')2 and venom antigens, as the terminal half-life and volume of distribution of the F(ab')2 in serum were comparable to that of venom antigens (p > 0.05). Infusion of an additional 2 ml of NPAV was able to prevent resurgence of the serum venom antigen level, resulting in a substantial decrease (67.1%) of the total amount of circulating venom antigens over time course of envenomation. Our results showed that the neutralization potency of NPAV determined by neutralization assay in mice may not be an adequate indicator of its capability to modulate venom kinetics in relation to its in vivo efficacy to neutralize venom toxicity. The findings also support the recommendation of giving high initial dose of NPAV in cobra envenomation, with repeated doses as clinically indicated in the presence of rebound antigenemia and symptom recurrence.
    Matched MeSH terms: Models, Biological
  15. Yahya N, Ebert MA, Bulsara M, House MJ, Kennedy A, Joseph DJ, et al.
    Med Phys, 2016 May;43(5):2040.
    PMID: 27147316 DOI: 10.1118/1.4944738
    Given the paucity of available data concerning radiotherapy-induced urinary toxicity, it is important to ensure derivation of the most robust models with superior predictive performance. This work explores multiple statistical-learning strategies for prediction of urinary symptoms following external beam radiotherapy of the prostate.
    Matched MeSH terms: Models, Biological
  16. Yahya N, Ebert MA, Bulsara M, Kennedy A, Joseph DJ, Denham JW
    Radiother Oncol, 2016 08;120(2):339-45.
    PMID: 27370204 DOI: 10.1016/j.radonc.2016.05.010
    BACKGROUND AND PURPOSE: Most predictive models are not sufficiently validated for prospective use. We performed independent external validation of published predictive models for urinary dysfunctions following radiotherapy of the prostate.

    MATERIALS/METHODS: Multivariable models developed to predict atomised and generalised urinary symptoms, both acute and late, were considered for validation using a dataset representing 754 participants from the TROG 03.04-RADAR trial. Endpoints and features were harmonised to match the predictive models. The overall performance, calibration and discrimination were assessed.

    RESULTS: 14 models from four publications were validated. The discrimination of the predictive models in an independent external validation cohort, measured using the area under the receiver operating characteristic (ROC) curve, ranged from 0.473 to 0.695, generally lower than in internal validation. 4 models had ROC >0.6. Shrinkage was required for all predictive models' coefficients ranging from -0.309 (prediction probability was inverse to observed proportion) to 0.823. Predictive models which include baseline symptoms as a feature produced the highest discrimination. Two models produced a predicted probability of 0 and 1 for all patients.

    CONCLUSIONS: Predictive models vary in performance and transferability illustrating the need for improvements in model development and reporting. Several models showed reasonable potential but efforts should be increased to improve performance. Baseline symptoms should always be considered as potential features for predictive models.

    Matched MeSH terms: Models, Biological*
  17. Yaakop AS, Chan KG, Ee R, Lim YL, Lee SK, Manan FA, et al.
    Sci Rep, 2016 09 19;6:33660.
    PMID: 27641516 DOI: 10.1038/srep33660
    Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.
    Matched MeSH terms: Models, Biological
  18. Yaacob H, Karim I, Wahab A, Kamaruddin N
    PMID: 23367309 DOI: 10.1109/EMBC.2012.6347374
    Emotions are ambiguous. Many techniques have been employed to perform emotion prediction and to understand emotional elicitations. Brain signals measured using electroencephalogram (EEG) are also used in studies about emotions. Using KDE as feature extraction technique and MLP for performing supervised learning on the brain signals. It has shown that all channels in EEG can capture emotional experience. In addition it was also indicated that emotions are dynamic as represented by the level of valence and the intensity of arousal. Such findings are useful in biomedical studies, especially in dealing with emotional disorders which can results in using a two-channel EEG device for neurofeedback applications.
    Matched MeSH terms: Models, Biological
  19. Ya'aini N, Amin NA, Asmadi M
    Bioresour Technol, 2012 Jul;116:58-65.
    PMID: 22609656 DOI: 10.1016/j.biortech.2012.03.097
    Conversion of glucose, empty fruit bunch (efb) and kenaf to levulinic acid over a new hybrid catalyst has been investigated in this study. The characterization and catalytic performance results revealed that the physico-chemical properties of the new hybrid catalyst comprised of chromium chloride and HY zeolite increased the levulinic acid production from glucose compared to the parent catalysts. Optimization of the glucose conversion process using two level full factorial designs (2(3)) with two center points reported 55.2% of levulinic acid yield at 145.2 °C, 146.7 min and 12.0% of reaction temperature, reaction time and catalyst loading, respectively. Subsequently, the potential of efb and kenaf for producing levulinic acid at the optimum conditions was established after 53.2% and 66.1% of efficiencies were reported. The observation suggests that the hybrid catalyst has a potential to be used in biomass conversion to levulinic acid.
    Matched MeSH terms: Models, Biological
  20. Xin LZ, Govindasamy V, Musa S, Abu Kasim NH
    Med Hypotheses, 2013 Oct;81(4):704-6.
    PMID: 23932760 DOI: 10.1016/j.mehy.2013.07.032
    Dental tissues contains stem cells or progenitors that have high proliferative capacity, are clonogenic in vitro and demonstrate the ability to differentiate to multiple type cells involving neurons, bone, cartilage, fat and smooth muscle. Numerous experiments have demonstrated that the multipotent stem cells are not rejected by immune system and therefore it may be possible to use these cells in allogeneic settings. In addition, these remarkable cells are easily abundantly available couple with less invasive procedure in isolating comparing to bone marrow aspiration. Here we proposed dental stem cells as candidate for cardiac regeneration based on its immature characteristic and propensity towards cardiac lineage via PI3-Kinase/Aktsignalling pathway.
    Matched MeSH terms: Models, Biological*
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