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Modeling of oscillatory bursting activity of pancreatic beta-cells under regulated glucose stimulation

Chew YH, Shia YL, Lee CT, Majid FA, Chua LS, Sarmidi MR, et al.

Mol Cell Endocrinol, 2009 Aug 13;307(1-2):57-67.
PMID: 19524127 DOI: 10.1016/j.mce.2009.03.005

A mathematical model to describe the oscillatory bursting activity of pancreatic beta-cells is combined with a model of glucose regulation system in this work to study the bursting pattern under regulated extracellular glucose stimulation. The bursting electrical activity in beta-cells is crucial for the release of insulin, which acts to regulate the blood glucose level. Different types of bursting pattern have been observed experimentally in glucose-stimulated islets both in vivo and in vitro, and the variations in these patterns have been linked to changes in glucose level. The combined model in this study enables us to have a deeper understanding on the regime change of bursting pattern when glucose level changes due to hormonal regulation, especially in the postprandial state. This is especially important as the oscillatory components of electrical activity play significant physiological roles in insulin secretion and some components have been found to be lost in type 2 diabetic patients.

Matched MeSH terms: Models, Biological*
Coordination of Ce(III) and Nd(III) with pentaethylene glycol in the presence of picrate anion: spectroscopic and X-ray structural studies

Kusrini E, Saleh MI, Lecomte C

Spectrochim Acta A Mol Biomol Spectrosc, 2009 Sep 15;74(1):120-6.
PMID: 19560960 DOI: 10.1016/j.saa.2009.05.024

(1)H NMR evidence for direct coordination between the Ln(III) ion and the oxygen atoms of the pentaethylene glycol (EO5) ligand and the picrate anion (Pic) in [Ln(Pic)(2)(EO5)][Pic] {Ln=Ce and Nd} complexes are confirmed by single X-ray diffraction. No dissociation of Ln-O bonds in dimethyl sulfoxide-d solution was observed in NMR studies conducted at different temperatures ranging 25-100 degrees C. The Ln(III) ion was chelated to nine oxygen atoms from the EO5 ligand in a hexadentate manner and the two Pic anions in each bidentate and monodentate modes. Both compounds are isostructural and crystallized in monoclinic with space group P2(1)/c. Coordination environment around the Ce1 and Nd1 atoms can be described as tricapped trigonal prismatic and monocapped square antiprismatic geometries, respectively. The crystal packing of the complexes have stabilized by one dimensional (1D) chains along the [001] direction to form intermolecular O-Hcdots, three dots, centeredO and C-Hcdots, three dots, centeredO hydrogen bonding. The molar conductance of the complexes in DMSO solution indicated that both compounds are ionic. The complexes had a good thermal stability. Under the UV-excitation, these complexes exhibited the red-shift emission.

Matched MeSH terms: Models, Biological
Fulltext In vitro fermentation of broiler cecal content: the role of lactobacilli and pH value on the composition of microbiota and end products fermentation

Meimandipour A, Shuhaimi M, Hair-Bejo M, Azhar K, Kabeir BM, Rasti B, et al.

Lett Appl Microbiol, 2009 Oct;49(4):415-20.
PMID: 19725887 DOI: 10.1111/j.1472-765X.2009.02674.x

To assess the probiotic effects of Lactobacillus agilis JCM 1048 and L. salivarius ssp. salicinius JCM 1230 and the pH on the cecal microflora of chicken and metabolic end products.

Matched MeSH terms: Models, Biological
Simulation of motorcycle crashes with w-beam guardrail: injury patterns and analysis

Ibitoye AB, Hamouda AM, Wong SV, Umar RS

Proc Inst Mech Eng H, 2009 Nov;223(8):1033-40.
PMID: 20092099

This study uses computer simulations to study the impact of a motorcycle with the conventional w-beam guardrail. A three-dimensional computer simulation of a scaled hybrid III 50th-percentile male dummy mounted on a motorcycle and colliding with a w-beam guardrail is carried out. A multi-body model of the motorcycle and finite element model of the guardrail are developed using commercially available software. The simulation model is validated with a physical crash test conducted with same initial impact configurations. Impacts at speeds of 32, 48, and 60 km/h at an impact angle at 45 degrees are considered. The predicted forces and accelerations are compared with the biomechanical limits for each body part and the risk of injury to the rider are evaluated. Speed was found to have a significant influence on the level of injury to the head, neck, chest, and femur. A significant reduction of the severity of injuries was found when the impact speed was reduced from 60 to 32km/h. The accelerations experienced by the head and chest are found to be higher than safe levels for impact speeds of 48 and 60 km/h. The biomechanical limit for the right femur is exceeded at all three considered impact speeds. Neck injuries are also a concern, with the predicted tension values and neck bending extent being higher than the biomechanical limit for the 60 km/h impact speed. In light of these results, it is suggested that the design of guardrails should be reviewed with a focus on the safety of motorcyclists.

Matched MeSH terms: Models, Biological*
Circadian and solar clocks interact in seasonal flowering

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
Fulltext Niches, body sizes, and the disassembly of mammal communities on the Sunda Shelf islands

Okie JG, Brown JH

Proc Natl Acad Sci U S A, 2009 Nov 17;106 Suppl 2:19679-84.
PMID: 19805179 DOI: 10.1073/pnas.0901654106

The rising sea level at the end of the Pleistocene that created the islands of the Sunda Shelf in Indonesia and Malaysia provides a natural experiment in community disassembly and offers insights into the effects of body size and niches on abundance, distribution, and diversity. Since isolation, terrestrial mammal communities of these islands have been reduced by extinction, with virtually no offsetting colonization. We document three empirical patterns of disassembly, all of which are significantly different from null models of random assembly: (i) a diversity-area relationship: the number of taxa is strongly and positively correlated with island area; (ii) nested subset composition: species that occur on small islands tend to be subsets of more diverse communities inhabiting larger islands; and (iii) body size distributions: species of intermediate body sizes occur on the greatest number of islands, and smaller islands have smaller ranges of body sizes, caused by the absence of species of both very large and extremely small size. These patterns reveal the role of body size and other niche characteristics, such as habitat requirements and trophic status, in the differential susceptibility of taxa to extinction.

Matched MeSH terms: Models, Biological*
Fulltext A simple model to demonstrate the movements and the axes of the eyeball

Nayak S, Soumya KV

Adv Physiol Educ, 2009 Dec;33(4):356-7.
PMID: 19948688 DOI: 10.1152/advan.00047.2009
Matched MeSH terms: Models, Biological*
Fulltext Paternity analysis-based inference of pollen dispersal patterns, male fecundity variation, and influence of flowering tree density and general flowering magnitude in two dipterocarp species

Tani N, Tsumura Y, Kado T, Taguchi Y, Lee SL, Muhammad N, et al.

Ann Bot, 2009 Dec;104(7):1421-34.
PMID: 19808773 DOI: 10.1093/aob/mcp252

BACKGROUND AND AIMS: Knowledge of pollen dispersal patterns and variation of fecundity is essential to understanding plant evolutionary processes and to formulating strategies to conserve forest genetic resources. Nevertheless, the pollen dispersal pattern of dipterocarp, main canopy tree species in palaeo-tropical forest remains unclear, and flowering intensity variation in the field suggests heterogeneity of fecundity.
METHODS: Pollen dispersal patterns and male fecundity variation of Shorea leprosula and Shorea parvifolia ssp. parvifolia on Peninsular Malaysian were investigated during two general flowering seasons (2001 and 2002), using a neighbourhood model modified by including terms accounting for variation in male fecundity among individual trees to express heterogeneity in flowering.
KEY RESULTS: The pollen dispersal patterns of the two dipterocarp species were affected by differences in conspecific tree flowering density, and reductions in conspecific tree flowering density led to an increased selfing rate. Active pollen dispersal and a larger number of effective paternal parents were observed for both species in the season of greater magnitude of general flowering (2002).
CONCLUSIONS: The magnitude of general flowering, male fecundity variation, and distance between pollen donors and mother trees should be taken into account when attempting to predict the effects of management practices on the self-fertilization and genetic structure of key tree species in tropical forest, and also the sustainability of possible management strategies, especially selective logging regimes.

Matched MeSH terms: Models, Biological
Organ- and endotheliotropism of Nipah virus infections in vivo and in vitro

Maisner A, Neufeld J, Weingartl H

Thromb. Haemost., 2009 Dec;102(6):1014-23.
PMID: 19967130 DOI: 10.1160/TH09-05-0310

Nipah virus (NiV) is a highly pathogenic paramyxovirus that was first isolated in 1999 during an outbreak in Malaysia. In contrast to other paramyxoviruses NiV infects many mammalian species. Because of its zoonotic potential, the high pathogenicity and the lack of therapeutic treatment, NiV was classified as a biosafety level 4 pathogen. In humans NiV causes a severe acute encephalitis whereas in some animal hosts respiratory symptoms are predominantly observed. Despite the differences in the clinical outcome, microvascular endothelial cell damage predominantly underlies the pathological changes in NiV infections in all susceptible host species. NiV generally induces a pronounced vasculitis which is primarily characterised by endothelial cell necrosis and inflammatory cell infiltration. For future developments of specific antiviral therapies or vaccines, a detailed understanding of the molecular basis of NiV pathogenesis is required. This article reviews the current knowledge about natural and experimental infections in different mammals, focusing on the main organ and cell tropism in vivo, and summarises some recent studies in cell culture on the role of ephrin-B2 and -B3 receptors in NiV infection of endothelial cells.

Matched MeSH terms: Models, Biological
Interface pressure profile analysis for patellar tendon-bearing socket and hydrostatic socket

Moo EK, Osman NA, Pingguan-Murphy B, Abas WA, Spence WD, Solomonidis SE

Acta Bioeng Biomech, 2009;11(4):37-43.
PMID: 20405814

Conventionally, patellar tendon-bearing (PTB) sockets, which need high dexterity of prosthetist, are widely used. Lack of chartered and experienced prosthetist has often led to painful experience of wearing prosthesis and this will in turn deter the patients to wear the prosthesis, which will further aggravate stump shrinkage. Thus, the hydrostatic socket which demands relatively lower level of fabricating skill is proposed to replace the PTB socket in order to produce the equivalent, if not better, quality of support to the amputee patients. Both sockets' pressure profiles are studied and compared using finite element analysis (FEA) software. Three-dimensional models of both sockets were developed using MIMICS software. The analysis results showed that hydrostatic socket did exhibit more uniform pressure profiles than that of PTB socket. PTB socket showed pressure concentration near the proximal brim of the socket and also at the distal fibula. It was also found that the pressure magnitude in hydrostatic socket is relatively lower than that of PTB socket.

Matched MeSH terms: Models, Biological
Respirometric analysis of activated sludge models from palm oil mill effluent

Damayanti A, Ujang Z, Salim MR, Olsson G, Sulaiman AZ

Bioresour Technol, 2010 Jan;101(1):144-9.
PMID: 19734044 DOI: 10.1016/j.biortech.2009.08.034

Activated sludge models (ASMs) have been widely used as a basis for further model development in wastewater treatment processes. Values for parameters to be used are vital for the accuracy of the modeling approach. A continuous stirred tank reactor (CSTR), as open respirometer with continuous flow for 20 h is used in ASMs. The dissolved oxygen (DO) profile for 11 days was monitored. It was found the mass transfer coefficient K(La) is 0.3 h(-1) during lag and start feed phase and 0.01 h(-1) during stop feed phase, while the heterotrophic yield coefficient Y(H) is 0.44. Some of the chemical oxygen demand (COD) fractionations of palm oil mill effluent (POME) using respirometric test in ASM models are S(s) 50 mg/L, S(I) 16,600 mg/L, X(S) 25,550 mg/L, and X(I) 2,800 mg/L. The comparison of experimental and ASM1 from OUR concentration is found to fit well.

Matched MeSH terms: Models, Biological*
Thermal noise due to surface-charge effects within the Debye layer of endogenous structures in dendrites

Poznanski RR

Phys Rev E Stat Nonlin Soft Matter Phys, 2010 Feb;81(2 Pt 1):021902.
PMID: 20365590

An assumption commonly used in cable theory is revised by taking into account electrical amplification due to intracellular capacitive effects in passive dendritic cables. A generalized cable equation for a cylindrical volume representation of a dendritic segment is derived from Maxwell's equations under assumptions: (i) the electric-field polarization is restricted longitudinally along the cable length; (ii) extracellular isopotentiality; (iii) quasielectrostatic conditions; and (iv) homogeneous medium with constant conductivity and permittivity. The generalized cable equation is identical to Barenblatt's equation arising in the theory of infiltration in fissured strata with a known analytical solution expressed in terms of a definite integral involving a modified Bessel function and the solution to a linear one-dimensional classical cable equation. Its solution is used to determine the impact of thermal noise on voltage attenuation with distance at any particular time. A regular perturbation expansion for the membrane potential about the linear one-dimensional classical cable equation solution is derived in terms of a Green's function in order to describe the dynamics of free charge within the Debye layer of endogenous structures in passive dendritic cables. The asymptotic value of the first perturbative term is explicitly evaluated for small values of time to predict how the slowly fluctuating (in submillisecond range) electric field attributed to intracellular capacitive effects alters the amplitude of the membrane potential. It was found that capacitive effects are almost negligible for cables with electrotonic lengths L>0.5 , contributes up to 10% of the signal for cables with electrotonic lengths in the range between 0.25

Matched MeSH terms: Models, Biological*
Population pharmacokinetic modelling of repaglinide in healthy volunteers by using Non-Parametric Adaptive Grid Algorithm

Ruzilawati AB, Mohd Suhaimi AW, Gan SH

J Clin Pharm Ther, 2010 Feb;35(1):105-12.
PMID: 20175819 DOI: 10.1111/j.1365-2710.2009.01042.x

To estimate population pharmacokinetic parameters of repaglinide in 121 healthy Malaysian volunteers.

Matched MeSH terms: Models, Biological
A standard quantitative method to measure acid tolerance of probiotic cells

Chan ES, Lee PP, Ravindra P, Krishnaiah K, Voo WP

Appl Microbiol Biotechnol, 2010 Mar;86(1):385-91.
PMID: 20033402 DOI: 10.1007/s00253-009-2384-y

The aim of this work was to develop a standard quantitative method to measure the acid tolerance of probiotic cells when exposed to a simulated gastric fluid. Three model strains of different cell concentrations were exposed to a standard simulated gastric fluid of fixed volume. The fluid pH ranged from pH 1.5 to 2.5. In general, the death kinetics followed an exponential trend. The overall death constant, k (d), for all strains was found to be in a power relationship with the pH value and the initial cell concentration, and it can be expressed as k(d)=k(AII) (pH(-9.0)N(0)(-0.19)) where k (AII) is defined as the acid intolerance indicator and N (0) is the initial cell concentration (CFU/ml). This equation was validated with the experimental data with an average R (2) of 0.98. The acid intolerance of cells can be quantitatively expressed by the k (AII) values, where higher value indicates higher intolerance. In conclusion, a standard quantitative method has been developed to measure the acid tolerance of probiotic cells. This could facilitate the selection of probiotic strains and processing technologies.

Matched MeSH terms: Models, Biological
Experimental investigation of the flow of bile in patient specific cystic duct models

Al-Atabi M, Chin SB, Luo XY

J Biomech Eng, 2010 Apr;132(4):041003.
PMID: 20387966 DOI: 10.1115/1.4001043

Three-dimensional scaled-up transparent models of three human cystic ducts were prepared on the basis of anatomical specimens. The measurement of pressure drop across the cystic duct models and visualization of the flow structures within these ducts were performed at conditions replicating the physiological state. The flow visualization study confirmed the laminar nature of the flow of bile inside the cystic duct and values of pressure drop coefficient (Cp) decreased as the Reynolds number (Re) increased. The three tested models showed comparable behavior for the curve of Reynolds number versus the pressure drop coefficient. The results show that the tested cystic ducts have both increased pressure drop and complicated flow structures when compared with straight conduits. High resistance in a cystic duct may indicate that the gallbladder has to exert large force in expelling bile to the cystic duct. For patients with diseased gallbladder, and even in healthy persons, gallbladder is known to stiffen with age and it may lose its compliance or flexibility. A high resistance cystic duct coupled with a stiffened gallbladder may result in prolonged stasis of bile in the gallbladder, which is assumed to encourage the formation of gallstones.

Matched MeSH terms: Models, Biological*
A kinetic study of autohydrogenotrophic denitrification at the optimum pH and sodium bicarbonate dose

Ghafari S, Hasan M, Aroua MK

Bioresour Technol, 2010 Apr;101(7):2236-42.
PMID: 20015639 DOI: 10.1016/j.biortech.2009.11.068

In this study the kinetics of autohydrogenotrophic denitrification was studied under optimum solution pH and bicarbonate concentration. The optimal pH and bicarbonate concentration were firstly obtained using a design of experiment (DOE) methodology. For this purpose a total of 11 experiments were carried out. Sodium bicarbonate concentrations ranging of 20-2000 mg/L and pH values from 6.5 to 8.5 were used in the optimization runs. It was found that the pH has a more pronounced effect on the denitrification process as compared to the bicarbonate dose. The developed quadratic model predicted the optimum conditions at pH 8 and 1100 mg NaHCO(3)/L. Using these optimal conditions, the kinetics of denitrification for nitrate and nitrite degradation were investigated in separate experiments. Both processes were found to follow a zero order kinetic model. The ultimate specific degradation rates for nitrate and nitrite remediation were 29.60 mg NO(3)(-)-N/g MLVSS/L and 34.85 mg NO(3)(-)-N/g MLVSS/L respectively, when hydrogen was supplied every 0.5h.

Matched MeSH terms: Models, Biological
Fulltext Population pharmacokinetics of vancomycin in premature Malaysian neonates: identification of predictors for dosing determination

Lo YL, van Hasselt JG, Heng SC, Lim CT, Lee TC, Charles BG

Antimicrob Agents Chemother, 2010 Jun;54(6):2626-32.
PMID: 20385872 DOI: 10.1128/AAC.01370-09

The present study determined the pharmacokinetic profile of vancomycin in premature Malaysian infants. A one-compartment infusion model with first-order elimination was fitted to serum vancomycin concentration data (n = 835 points) obtained retrospectively from the drug monitoring records of 116 premature newborn infants. Vancomycin concentrations were estimated by a fluorescence polarization immunoassay. Population and individual estimates of clearance and distribution volume and the factors which affected the variability observed for the values of these parameters were obtained using a population pharmacokinetic modeling approach. The predictive performance of the population model was evaluated by visual inspections of diagnostic plots and nonparametric bootstrapping with replacement. Dosing guidelines targeting a value of > or =400 for the area under the concentration-time curve over 24 h in the steady state divided by the MIC (AUC(24)/MIC ratio) were explored using Monte Carlo simulation. Body size (weight), postmenstrual age, and small-for-gestational-age status are important factors explaining the between-subject variability of vancomycin pharmacokinetic parameter values for premature neonates. The typical population parameter estimates of clearance and distribution volume for a 1-kg premature appropriate-for-gestational-age neonate with a postmenstrual age of 30 weeks were 0.0426 liters/h and 0.523 liters, respectively. There was a 20% reduction in clearance for small-for-gestational-age infants compared to the level for the appropriate-for-gestational-age control. Dosage regimens based on a priori target response values were formulated. In conclusion, the pharmacokinetic parameter values for vancomycin in premature Malaysian neonates were estimated. Improved dosage regimens based on a priori target response values were formulated by incorporating body size, postmenstrual age, and small-for-gestational-age status, using Monte Carlo simulations with the model-estimated pharmacokinetic parameter values.

Matched MeSH terms: Models, Biological
Utilization of sludge palm oil as a novel substrate for biosurfactant production

Wan Nawawi WM, Jamal P, Alam MZ

Bioresour Technol, 2010 Dec;101(23):9241-7.
PMID: 20674345 DOI: 10.1016/j.biortech.2010.07.024

This paper introduces sludge palm oil (SPO) as a novel substrate for biosurfactant production by liquid state fermentation. Potential strains of microorganism were isolated from various hydrocarbon-based sources at palm oil mill and screened for biosurfactant production with the help of drop collapse method and surface tension activity. Out of 22 isolates of microorganism, the strain S02 showed the highest bacterial growth with a surface tension of 36.2 mN/m and was therefore, selected as a potential biosurfactant producing microorganism. Plackett-Burman experimental design was employed to determine the important nutritional requirement for biosurfactant production by the selected strain under controlled conditions. Six out of 11 factors of the production medium were found to significantly affect the biosurfactant production. K(2)HPO(4) had a direct proportional correlation with the biosurfactant production while sucrose, glucose, FeSO(4), MgSO(4), and NaNO(3) showed inversely proportional relationship with biosurfactant production in the selected experimental range.

Matched MeSH terms: Models, Biological
Small-sample estimation of species richness applied to forest communities

Hwang WH, Shen TJ

Biometrics, 2010 Dec;66(4):1052-60.
PMID: 20002401 DOI: 10.1111/j.1541-0420.2009.01371.x

Many well-known methods are available for estimating the number of species in a forest community. However, most existing methods result in considerable negative bias in applications, where field surveys typically represent only a small fraction of sampled communities. This article develops a new method based on sampling with replacement to estimate species richness via the generalized jackknife procedure. The proposed estimator yields small bias and reasonably accurate interval estimation even with small samples. The performance of the proposed estimator is compared with several typical estimators via simulation study using two complete census datasets from Panama and Malaysia.

Matched MeSH terms: Models, Biological
Fulltext In vitro and in vivo anti-inflammatory activity of 17-O-acetylacuminolide through the inhibition of cytokines, NF-κB translocation and IKKβ activity

Achoui M, Appleton D, Abdulla MA, Awang K, Mohd MA, Mustafa MR

PLoS One, 2010;5(12):e15105.
PMID: 21152019 DOI: 10.1371/journal.pone.0015105

17-O-acetylacuminolide (AA), a diterpenoid labdane, was isolated for the first time from the plant species Neouvaria foetida. The anti-inflammatory effects of this compound were studied both in vitro and in vivo.

Matched MeSH terms: Models, Biological

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