Displaying publications 1 - 20 of 405 in total

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  1. Syahrom A, Abdul Kadir MR, Harun MN, Öchsner A
    Med Eng Phys, 2015 Jan;37(1):77-86.
    PMID: 25523865 DOI: 10.1016/j.medengphy.2014.11.001
    Artificial bone is a suitable alternative to autografts and allografts, however their use is still limited. Though there were numerous reports on their structural properties, permeability studies of artificial bones were comparably scarce. This study focused on the development of idealised, structured models of artificial cancellous bone and compared their permeability values with bone surface area and porosity. Cancellous bones from fresh bovine femur were extracted and cleaned following an established protocol. The samples were scanned using micro-computed tomography (μCT) and three-dimensional models of the cancellous bones were reconstructed for morphology study. Seven idealised and structured cancellous bone models were then developed and fabricated via rapid prototyping technique. A test-rig was developed and permeability tests were performed on the artificial and real cancellous bones. The results showed a linear correlation between the permeability and the porosity as well as the bone surface area. The plate-like idealised structure showed a similar value of permeability to the real cancellous bones.
    Matched MeSH terms: Models, Biological*
  2. Trusch F, Loebach L, Wawra S, Durward E, Wuensch A, Iberahim NA, et al.
    Nat Commun, 2018 06 14;9(1):2347.
    PMID: 29904064 DOI: 10.1038/s41467-018-04796-3
    The animal-pathogenic oomycete Saprolegnia parasitica causes serious losses in aquaculture by infecting and killing freshwater fish. Like plant-pathogenic oomycetes, S. parasitica employs similar infection structures and secretes effector proteins that translocate into host cells to manipulate the host. Here, we show that the host-targeting protein SpHtp3 enters fish cells in a pathogen-independent manner. This uptake process is guided by a gp96-like receptor and can be inhibited by supramolecular tweezers. The C-terminus of SpHtp3 (containing the amino acid sequence YKARK), and not the N-terminal RxLR motif, is responsible for the uptake into host cells. Following translocation, SpHtp3 is released from vesicles into the cytoplasm by another host-targeting protein where it degrades nucleic acids. The effector translocation mechanism described here, is potentially also relevant for other pathogen-host interactions as gp96 is found in both animals and plants.
    Matched MeSH terms: Models, Biological
  3. Gavai AK, Supandi F, Hettling H, Murrell P, Leunissen JA, van Beek JH
    PLoS One, 2015;10(3):e0119016.
    PMID: 25806817 DOI: 10.1371/journal.pone.0119016
    Predicting the distribution of metabolic fluxes in biochemical networks is of major interest in systems biology. Several databases provide metabolic reconstructions for different organisms. Software to analyze flux distributions exists, among others for the proprietary MATLAB environment. Given the large user community for the R computing environment, a simple implementation of flux analysis in R appears desirable and will facilitate easy interaction with computational tools to handle gene expression data. We extended the R software package BiGGR, an implementation of metabolic flux analysis in R. BiGGR makes use of public metabolic reconstruction databases, and contains the BiGG database and the reconstruction of human metabolism Recon2 as Systems Biology Markup Language (SBML) objects. Models can be assembled by querying the databases for pathways, genes or reactions of interest. Fluxes can then be estimated by maximization or minimization of an objective function using linear inverse modeling algorithms. Furthermore, BiGGR provides functionality to quantify the uncertainty in flux estimates by sampling the constrained multidimensional flux space. As a result, ensembles of possible flux configurations are constructed that agree with measured data within precision limits. BiGGR also features automatic visualization of selected parts of metabolic networks using hypergraphs, with hyperedge widths proportional to estimated flux values. BiGGR supports import and export of models encoded in SBML and is therefore interoperable with different modeling and analysis tools. As an application example, we calculated the flux distribution in healthy human brain using a model of central carbon metabolism. We introduce a new algorithm termed Least-squares with equalities and inequalities Flux Balance Analysis (Lsei-FBA) to predict flux changes from gene expression changes, for instance during disease. Our estimates of brain metabolic flux pattern with Lsei-FBA for Alzheimer's disease agree with independent measurements of cerebral metabolism in patients. This second version of BiGGR is available from Bioconductor.
    Matched MeSH terms: Models, Biological*
  4. Wang S, Loreau M, Arnoldi JF, Fang J, Rahman KA, Tao S, et al.
    Nat Commun, 2017 May 19;8:15211.
    PMID: 28524860 DOI: 10.1038/ncomms15211
    The spatial scaling of stability is key to understanding ecological sustainability across scales and the sensitivity of ecosystems to habitat destruction. Here we propose the invariability-area relationship (IAR) as a novel approach to investigate the spatial scaling of stability. The shape and slope of IAR are largely determined by patterns of spatial synchrony across scales. When synchrony decays exponentially with distance, IARs exhibit three phases, characterized by steeper increases in invariability at both small and large scales. Such triphasic IARs are observed for primary productivity from plot to continental scales. When synchrony decays as a power law with distance, IARs are quasilinear on a log-log scale. Such quasilinear IARs are observed for North American bird biomass at both species and community levels. The IAR provides a quantitative tool to predict the effects of habitat loss on population and ecosystem stability and to detect regime shifts in spatial ecological systems, which are goals of relevance to conservation and policy.
    Matched MeSH terms: Models, Biological*
  5. Slik JW, Aiba S, Bastian M, Brearley FQ, Cannon CH, Eichhorn KA, et al.
    Proc Natl Acad Sci U S A, 2011 Jul 26;108(30):12343-7.
    PMID: 21746913 DOI: 10.1073/pnas.1103353108
    The marked biogeographic difference between western (Malay Peninsula and Sumatra) and eastern (Borneo) Sundaland is surprising given the long time that these areas have formed a single landmass. A dispersal barrier in the form of a dry savanna corridor during glacial maxima has been proposed to explain this disparity. However, the short duration of these dry savanna conditions make it an unlikely sole cause for the biogeographic pattern. An additional explanation might be related to the coarse sandy soils of central Sundaland. To test these two nonexclusive hypotheses, we performed a floristic cluster analysis based on 111 tree inventories from Peninsular Malaysia, Sumatra, and Borneo. We then identified the indicator genera for clusters that crossed the central Sundaland biogeographic boundary and those that did not cross and tested whether drought and coarse-soil tolerance of the indicator genera differed between them. We found 11 terminal floristic clusters, 10 occurring in Borneo, 5 in Sumatra, and 3 in Peninsular Malaysia. Indicator taxa of clusters that occurred across Sundaland had significantly higher coarse-soil tolerance than did those from clusters that occurred east or west of central Sundaland. For drought tolerance, no such pattern was detected. These results strongly suggest that exposed sandy sea-bed soils acted as a dispersal barrier in central Sundaland. However, we could not confirm the presence of a savanna corridor. This finding makes it clear that proposed biogeographic explanations for plant and animal distributions within Sundaland, including possible migration routes for early humans, need to be reevaluated.
    Matched MeSH terms: Models, Biological
  6. Kiyasudeen K, Ibrahim MH, Muhammad SA, Ismail SA, Gonawan FN, Zuknik MH
    Environ Sci Pollut Res Int, 2018 Nov;25(31):31062-31070.
    PMID: 30187407 DOI: 10.1007/s11356-018-3074-z
    Earthworms are commonly referred as environmental engineers and their guts are often compared with chemical reactors. However, modeling experiments to substantiate it are lacking. The aim of this study was to use established reactor models, particularly PFR, on the gut of the vermicomposting earthworm Eudrilus eugeniae to understand more on its digestion. To achieve the objective, a mathematical model based on first-order kinetics was framed and used to determine the pattern of digestion rates of nutrient indicators, namely total carbon (%), total nitrogen (%), C/N ratio, 13C (‰), and 15N (‰) at five intersections (pre-intestine, foregut, midgut A, midgut B, and hindgut) along the gut of E. eugeniae. The experimental results revealed that the concentrations of TC, TN, 13C, and 15N decreased during gut transit, whereas C/N ratio increased. The first-order model demonstrated that all the nutrients exhibit a linear pattern of digestion during gut transit, which supports the PFR model. On this basis, the present study concludes that the gut of E. eugeniae functions as PFR.
    Matched MeSH terms: Models, Biological*
  7. Muniyandi RC, Zin AM
    Pak J Biol Sci, 2011 Dec 15;14(24):1100-8.
    PMID: 22335049
    Ligand-Receptor Networks of TGF-beta plays essential role in transmitting a wide range of extracellular signals that affect many cellular processes such as cell growth. However, the modeling of these networks with conventional approach such as ordinary differential equations has not taken into account, the spatial structure and stochastic behavior of processes involve in these networks. Membrane computing as the alternatives approach provides spatial structure for molecular computation in which processes are evaluated in a non-deterministic and maximally parallel way. This study is carried out to evaluate the membrane computing model of Ligand-Receptor Networks of TGF-beta with model checking approach. The results show that membrane computing model has sustained the behaviors and properties of Ligand-Receptor Networks of TGF-beta. This reinforce that membrane computing is capable in analyzing processes and behaviors in hierarchical structure of cell such as Ligand-Receptor Networks of TGF-beta better than the deterministic approach of conventional mathematical models.
    Matched MeSH terms: Models, Biological
  8. Wills C, Wang B, Fang S, Wang Y, Jin Y, Lutz J, et al.
    PLoS Comput Biol, 2021 Apr;17(4):e1008853.
    PMID: 33914731 DOI: 10.1371/journal.pcbi.1008853
    When Darwin visited the Galapagos archipelago, he observed that, in spite of the islands' physical similarity, members of species that had dispersed to them recently were beginning to diverge from each other. He postulated that these divergences must have resulted primarily from interactions with sets of other species that had also diverged across these otherwise similar islands. By extrapolation, if Darwin is correct, such complex interactions must be driving species divergences across all ecosystems. However, many current general ecological theories that predict observed distributions of species in ecosystems do not take the details of between-species interactions into account. Here we quantify, in sixteen forest diversity plots (FDPs) worldwide, highly significant negative density-dependent (NDD) components of both conspecific and heterospecific between-tree interactions that affect the trees' distributions, growth, recruitment, and mortality. These interactions decline smoothly in significance with increasing physical distance between trees. They also tend to decline in significance with increasing phylogenetic distance between the trees, but each FDP exhibits its own unique pattern of exceptions to this overall decline. Unique patterns of between-species interactions in ecosystems, of the general type that Darwin postulated, are likely to have contributed to the exceptions. We test the power of our null-model method by using a deliberately modified data set, and show that the method easily identifies the modifications. We examine how some of the exceptions, at the Wind River (USA) FDP, reveal new details of a known allelopathic effect of one of the Wind River gymnosperm species. Finally, we explore how similar analyses can be used to investigate details of many types of interactions in these complex ecosystems, and can provide clues to the evolution of these interactions.
    Matched MeSH terms: Models, Biological
  9. Saqib F, Ahmed MG, Janbaz KH, Dewanjee S, Jaafar HZ, Zia-Ul-Haq M
    PMID: 26354022 DOI: 10.1186/s12906-015-0837-7
    Murraya paniculata is traditionally used for management of gut, air way and cardiovascular disorders. The study was conducted for provision of pharmacological rationalization for folkloric uses of Murraya paniculata in gut, air way and cardiovascular problems.
    Matched MeSH terms: Models, Biological
  10. Tang BH, Guan Z, Allegaert K, Wu YE, Manolis E, Leroux S, et al.
    Clin Pharmacokinet, 2021 11;60(11):1435-1448.
    PMID: 34041714 DOI: 10.1007/s40262-021-01033-x
    BACKGROUND: Population pharmacokinetic evaluations have been widely used in neonatal pharmacokinetic studies, while machine learning has become a popular approach to solving complex problems in the current era of big data.

    OBJECTIVE: The aim of this proof-of-concept study was to evaluate whether combining population pharmacokinetic and machine learning approaches could provide a more accurate prediction of the clearance of renally eliminated drugs in individual neonates.

    METHODS: Six drugs that are primarily eliminated by the kidneys were selected (vancomycin, latamoxef, cefepime, azlocillin, ceftazidime, and amoxicillin) as 'proof of concept' compounds. Individual estimates of clearance obtained from population pharmacokinetic models were used as reference clearances, and diverse machine learning methods and nested cross-validation were adopted and evaluated against these reference clearances. The predictive performance of these combined methods was compared with the performance of two other predictive methods: a covariate-based maturation model and a postmenstrual age and body weight scaling model. Relative error was used to evaluate the different methods.

    RESULTS: The extra tree regressor was selected as the best-fit machine learning method. Using the combined method, more than 95% of predictions for all six drugs had a relative error of < 50% and the mean relative error was reduced by an average of 44.3% and 71.3% compared with the other two predictive methods.

    CONCLUSION: A combined population pharmacokinetic and machine learning approach provided improved predictions of individual clearances of renally cleared drugs in neonates. For a new patient treated in clinical practice, individual clearance can be predicted a priori using our model code combined with demographic data.

    Matched MeSH terms: Models, Biological*
  11. Stephenson NL, Das AJ, Condit R, Russo SE, Baker PJ, Beckman NG, et al.
    Nature, 2014 Mar 6;507(7490):90-3.
    PMID: 24429523 DOI: 10.1038/nature12914
    Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle--particularly net primary productivity and carbon storage--increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree's total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to undertand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.
    Matched MeSH terms: Models, Biological
  12. Cheah WL, Wan Muda WAM, Zamh ZH
    Rural Remote Health, 2010;10(1):1248.
    PMID: 20184392
    Many studies had shown that poor growth in children is associated with malnutrition. The underlying factors are diverse, multisectoral and interrelated, ranging from biological to social, cultural and economically related. Because the highest levels of under-nutrition worldwide are found in South Asia, it is essential that policymakers in the region understand the underlying determinants, in order to design effective public health intervention programs. This is especially so if public resources are limited. The purpose of this cross-sectional study was to examine causal relationships among the biological, behavioural and environmental factors related to malnutrition in children aged 5 years and under.
    Matched MeSH terms: Models, Biological
  13. Azman KF, Zakaria R
    Biogerontology, 2019 12;20(6):763-782.
    PMID: 31538262 DOI: 10.1007/s10522-019-09837-y
    To facilitate the process of aging healthily and prevent age-related health problems, efforts to properly understand aging mechanisms and develop effective and affordable anti-aging interventions are deemed necessary. Systemic administration of D-galactose has been established to artificially induce senescence in vitro and in vivo as well as for anti-aging therapeutic interventions studies. The aim of this article is to comprehensively discuss the use of D-galactose to generate a model of accelerated aging and its possible underlying mechanisms involved in different tissues/organs.
    Matched MeSH terms: Models, Biological*
  14. Taha M, Rahim F, Khan AA, Anouar EH, Ahmed N, Shah SAA, et al.
    Sci Rep, 2020 05 14;10(1):7969.
    PMID: 32409737 DOI: 10.1038/s41598-020-64729-3
    The current study describes synthesis of diindolylmethane (DIM) derivatives based-thiadiazole as a new class of urease inhibitors. Diindolylmethane is natural product alkaloid reported to use in medicinal chemistry extensively. Diindolylmethane-based-thiadiazole analogs (1-18) were synthesized and characterized by various spectroscopic techniques 1HNMR, 13C-NMR, EI-MS and evaluated for urease (jack bean urease) inhibitory potential. All compounds showed excellent to moderate inhibitory potential having IC50 value within the range of 0.50 ± 0.01 to 33.20 ± 1.20 µM compared with the standard thiourea (21.60 ± 0.70 µM). Compound 8 (IC50 = 0.50 ± 0.01 µM) was the most potent inhibitor amongst all derivatives. Structure-activity relationships have been established for all compounds. The key binding interactions of most active compounds with enzyme were confirmed through molecular docking studies.
    Matched MeSH terms: Models, Biological
  15. Chang SW, Abdul-Kareem S, Merican AF, Zain RB
    BMC Bioinformatics, 2013;14:170.
    PMID: 23725313 DOI: 10.1186/1471-2105-14-170
    Machine learning techniques are becoming useful as an alternative approach to conventional medical diagnosis or prognosis as they are good for handling noisy and incomplete data, and significant results can be attained despite a small sample size. Traditionally, clinicians make prognostic decisions based on clinicopathologic markers. However, it is not easy for the most skilful clinician to come out with an accurate prognosis by using these markers alone. Thus, there is a need to use genomic markers to improve the accuracy of prognosis. The main aim of this research is to apply a hybrid of feature selection and machine learning methods in oral cancer prognosis based on the parameters of the correlation of clinicopathologic and genomic markers.
    Matched MeSH terms: Models, Biological
  16. Salehi Z, Yusoff AL
    Radiat Prot Dosimetry, 2013;154(3):396-9.
    PMID: 23012482 DOI: 10.1093/rpd/ncs239
    A femur phantom made of wax and a real human bone was used to study the dose during radiographical procedures. The depth dose inside the phantom was determined using DOSXYZnrc, a Monte Carlo simulation software. The results were verified with measurements using TLD-100H. It was found that for 2.5 mm aluminium filtered 84-kVp X-rays, the radiation dose in the bone reached 57 % higher than the surface dose, i.e. 3.23 mGy as opposed to 2.06 mGy at the surface. The use of real bone introduces variations in the bone density in the DOSXYZnrc model, resulting in a lower attenuation effect than expected from solid bone tissues.
    Matched MeSH terms: Models, Biological*
  17. Agatonovic-Kustrin S, Beresford R, Yusof AP
    J Pharm Biomed Anal, 2001 May;25(2):227-37.
    PMID: 11275432
    A quantitative structure-human intestinal absorption relationship was developed using artificial neural network (ANN) modeling. A set of 86 drug compounds and their experimentally-derived intestinal absorption values used in this study was gathered from the literature and a total of 57 global molecular descriptors, including constitutional, topological, chemical, geometrical and quantum chemical descriptors, calculated for each compound. A supervised network with radial basis transfer function was used to correlate calculated molecular descriptors with experimentally-derived measures of human intestinal absorption. A genetic algorithm was then used to select important molecular descriptors. Intestinal absorption values (IA%) were used as the ANN's output and calculated molecular descriptors as the inputs. The best genetic neural network (GNN) model with 15 input descriptors was chosen, and the significance of the selected descriptors for intestinal absorption examined. Results obtained with the model that was developed indicate that lipophilicity, conformational stability and inter-molecular interactions (polarity, and hydrogen bonding) have the largest impact on intestinal absorption.
    Matched MeSH terms: Models, Biological
  18. Chen M, Zhang B, Li C, Kulaveerasingam H, Chew FT, Yu H
    Plant Physiol, 2015 Sep;169(1):391-402.
    PMID: 26152712 DOI: 10.1104/pp.15.00943
    Seed storage reserves mainly consist of starch, triacylglycerols, and storage proteins. They not only provide energy for seed germination and seedling establishment, but also supply essential dietary nutrients for human beings and animals. So far, the regulatory networks that govern the accumulation of seed storage reserves in plants are still largely unknown. Here, we show that TRANSPARENT TESTA GLABRA1 (TTG1), which encodes a WD40 repeat transcription factor involved in many aspects of plant development, plays an important role in mediating the accumulation of seed storage reserves in Arabidopsis (Arabidopsis thaliana). The dry weight of ttg1-1 embryos significantly increases compared with that of wild-type embryos, which is accompanied by an increase in the contents of starch, total protein, and fatty acids in ttg1-1 seeds. FUSCA3 (FUS3), a master regulator of seed maturation, binds directly to the TTG1 genomic region and suppresses TTG1 expression in developing seeds. TTG1 negatively regulates the accumulation of seed storage proteins partially through transcriptional repression of 2S3, a gene encoding a 2S albumin precursor. TTG1 also indirectly suppresses the expression of genes involved in either seed development or synthesis/modification of fatty acids in developing seeds. In addition, we demonstrate that the maternal allele of the TTG1 gene suppresses the accumulation of storage proteins and fatty acids in seeds. Our results suggest that TTG1 is a direct target of FUS3 in the framework of the regulatory hierarchy controlling seed filling and regulates the accumulation of seed storage proteins and fatty acids during the seed maturation process.
    Matched MeSH terms: Models, Biological
  19. Tripathi M, Zhang CW, Singh BK, Sinha RA, Moe KT, DeSilva DA, et al.
    Cell Death Dis, 2016 12 08;7(12):e2513.
    PMID: 27929536 DOI: 10.1038/cddis.2016.374
    Hyperhomocysteinemia (HHcy) is a well-known risk factor for stroke; however, its underlying molecular mechanism remains unclear. Using both mouse and cell culture models, we have provided evidence that impairment of autophagy has a central role in HHcy-induced cellular injury in the mouse brain. We observed accumulation of LC3B-II and p62 that was associated with increased MTOR signaling in human and mouse primary astrocyte cell cultures as well as a diet-induced mouse model of HHcy, HHcy decreased lysosomal membrane protein LAMP2, vacuolar ATPase (ATP6V0A2), and protease cathepsin D, suggesting that lysosomal dysfunction also contributed to the autophagic defect. Moreover, HHcy increased unfolded protein response. Interestingly, Vitamin B supplementation restored autophagic flux, alleviated ER stress, and reversed lysosomal dysfunction due to HHCy. Furthermore, the autophagy inducer, rapamycin was able to relieve ER stress and reverse lysosomal dysfunction caused by HHcy in vitro. Inhibition of autophagy by HHcy exacerbated cellular injury during oxygen and glucose deprivation and reperfusion (OGD/R), and oxidative stress. These effects were prevented by Vitamin B co-treatment, suggesting that it may be helpful in relieving detrimental effects of HHcy in ischemia/reperfusion or oxidative stress. Collectively, these findings show that Vitamin B therapy can reverse defects in cellular autophagy and ER stress due to HHcy; and thus may be a potential treatment to reduce ischemic damage caused by stroke in patients with HHcy.
    Matched MeSH terms: Models, Biological
  20. Kumar S, Neven LG, Yee WL
    J Econ Entomol, 2014 Jun;107(3):1032-44.
    PMID: 25026662
    Sweet cherries, Prunus avium (L.) L., grown in the western United States are exported to many countries around the world. Some of these countries have enforced strict quarantine rules and trade restrictions owing to concerns about the potential establishment and subsequent spread of western cherry fruit fly, Rhagoletis indifferens Curran (Diptera: Tephritidae), a major quarantine pest of sweet cherry. We used 1) niche models (CLIMEX and MaxEnt) to map the climatic suitability, 2) North Carolina State University-Animal and Plant Health Inspection Service Plant Pest Forecasting System to examine chilling requirement, and 3) host distribution and availability to assess the potential for establishment of R. indifferens in areas of western North America where it currently does not exist and eight current or potential fresh sweet cherry markets: Colombia, India, Indonesia, Malaysia, Taiwan, Thailand, Venezuela, and Vietnam. Results from niche models conformed well to the current distribution of R. indifferens in western North America. MaxEnt and CLIMEX models had high performance and predicted climatic suitability in some of the countries (e.g., Andean range in Colombia and Venezuela, northern and northeastern India, central Taiwan, and parts of Vietnam). However, our results showed no potential for establishment of R. indifferens in Colombia, Indonesia, Malaysia, Taiwan, Thailand, Venezuela, and Vietnam when the optimal chilling requirement to break diapause (minimum temperature < or = 3 degree C for at least 15 wk) was used as the criterion for whether establishment can occur. Furthermore, these countries have no host plant species available for R. indifferens. Our results can be used to make scientifically informed international trade decisions and negotiations by policy makers.
    Matched MeSH terms: Models, Biological
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