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1.
The question of whether there is a limit to the similarity of competing species has previously been investigated by a number of authors. These studies have all used the Lotka-Volterra model of competition, and have assumed that the competition coefficient αij may be calculated using the expression, αij = ∝ Ui(R) Uj(R) dR/∝ (Ui(R))2 dR. In this paper, the generality of this formula is questioned and two alternative expressions for αij are proposed. When these expressions are used in an analysis of limiting similarity, qualitatively different conclusions emerge regarding the existence and nature of this limit, using either deterministic or stochastic models. The relevance of these findings to theories of character convergence and similarity barriers is discussed. The available field evidence does not strongly support the validity of the formula for αij used in previous studies. Since a given method of calculating αij must be derived from a higher level model, it is suggested that the Lotka-Volterra model is not sufficient in an investigation of limiting similarity.  相似文献   

2.
Model-free analysis is a technique commonly used within the field of NMR spectroscopy to extract atomic resolution, interpretable dynamic information on multiple timescales from the R 1, R 2, and steady state NOE. Model-free approaches employ two disparate areas of data analysis, the discipline of mathematical optimisation, specifically the minimisation of a χ2 function, and the statistical field of model selection. By searching through a large number of model-free minimisations, which were setup using synthetic relaxation data whereby the true underlying dynamics is known, certain model-free models have been identified to, at times, fail. This has been characterised as either the internal correlation times, τ e , τ f , or τ s , or the global correlation time parameter, local τ m , heading towards infinity, the result being that the final parameter values are far from the true values. In a number of cases the minimised χ2 value of the failed model is significantly lower than that of all other models and, hence, will be the model which is chosen by model selection techniques. If these models are not removed prior to model selection the final model-free results could be far from the truth. By implementing a series of empirical rules involving inequalities these models can be specifically isolated and removed. Model-free analysis should therefore consist of three distinct steps: model-free minimisation, model-free model elimination, and finally model-free model selection. Failure has also been identified to affect the individual Monte Carlo simulations used within error analysis. Each simulation involves an independent randomised relaxation data set and model-free minimisation, thus simulations suffer from exactly the same types of failure as model-free models. Therefore, to prevent these outliers from causing a significant overestimation of the errors the failed Monte Carlo simulations need to be culled prior to calculating the parameter standard deviations.  相似文献   

3.
Tick-borne encephalitis virus (TBEV) is reciprocally transmitted between Ixodes ricinus ticks and small mammals. Recently, transmission between co-feeding ticks has been postulated as an epidemiological by important mechanism of perpetuating the agent. To empirically examine the question whether the “traditional” mode of transmission is sufficient to maintain enzootic TBEV transmission, the basic reproductive number R0 of TBEV could be estimated under this model for sites in which TBEV is enzootic. I propose an empirical estimator of R0 for TBEV which is based on longitudinal stage–specific local tick infestation densities assessed by live trapping of small mammals. A Gibbs sampler–based 95%–credibility interval is presented. When applied to published field data from TBEV enzootic sites sub–critical R0 estimates are obtained for both sites. I discuss potential shortcomings of this method and possible implications of these findings on the discussion of supplemental mechanisms of transmission. I thank Marc Lipsitch (Harvard School of Public Health, Boston, MA) who helped with an early version of this paper. I also thank Dr. Andrea Pugliese and two anonymous referees for their insightful comments and helpful suggestions.  相似文献   

4.
Summary In many instances, a subject can experience both a nonterminal and terminal event where the terminal event (e.g., death) censors the nonterminal event (e.g., relapse) but not vice versa. Typically, the two events are correlated. This situation has been termed semicompeting risks (e.g., Fine, Jiang, and Chappell, 2001 , Biometrika 88, 907–939; Wang, 2003 , Journal of the Royal Statistical Society, Series B 65, 257–273), and analysis has been based on a joint survival function of two event times over the positive quadrant but with observation restricted to the upper wedge. Implicitly, this approach entertains the idea of latent failure times and leads to discussion of a marginal distribution of the nonterminal event that is not grounded in reality. We argue that, similar to models for competing risks, latent failure times should generally be avoided in modeling such data. We note that semicompeting risks have more classically been described as an illness–death model and this formulation avoids any reference to latent times. We consider an illness–death model with shared frailty, which in its most restrictive form is identical to the semicompeting risks model that has been proposed and analyzed, but that allows for many generalizations and the simple incorporation of covariates. Nonparametric maximum likelihood estimation is used for inference and resulting estimates for the correlation parameter are compared with other proposed approaches. Asymptotic properties, simulations studies, and application to a randomized clinical trial in nasopharyngeal cancer evaluate and illustrate the methods. A simple and fast algorithm is developed for its numerical implementation.  相似文献   

5.
Quantitative expressions have been developed for systems such as yeast reductions where competing enzymes act on one substrate to yield two enantiomeric products. These expressions relate the observed stereochemical variables, the extent of conversion (C), the optical purity expressed as enantiomeric excess (ee), and the initial substrate concentration (A0) to the kinetic parameters KR and KS (apparent Michaelis constants) and y (VRVS, the ratio of maximal velocities) of such competing enzymes. The expressions have been experimentally verified using a purified competing enzyme system of l- and d-lactic dehydrogenases. Furthermore, the enantioselective reduction of β-keto esters by intact yeast cells has been examined by means of this kinetic analysis.  相似文献   

6.
(1R)‐Normetanephrine is the natural stereoisomeric substrate for sulfotransferase 1A3 (SULT1A3)‐catalyzed sulfonation. Nothing appears known on the enantioselectivity of the reaction despite its potential significance in the metabolism of adrenergic amines and in clinical biochemistry. We confronted the kinetic parameters of the sulfoconjugation of synthetic (1R)‐normetanephrine and (1S)‐normetanephrine by recombinant human SULT1A3 to a docking model of each normetanephrine enantiomer with SULT1A3 and the 3′‐phosphoadenosine‐5′‐phosphosulfate cofactor on the basis of molecular modeling and molecular dynamics simulations of the stability of the complexes. The KM, Vmax, and kcat values for the sulfonation of (1R)‐normetanephrine, (1S)‐normetanephrine, and racemic normetanephrine were similar. In silico models were consistent with these findings as they showed that the binding modes of the two enantiomers were almost identical. In conclusion, SULT1A3 is not substrate‐enantioselective toward normetanephrine, an unexpected finding explainable by a mutual adaptability between the ligands and SULT1A3 through an “induced‐fit model” in the catalytic pocket. Chirality, 25:28‐34, 2012.© 2012 Wiley Periodicals, Inc.  相似文献   

7.
We formulate a deterministic epidemic model for the spread of Hepatitis C containing an acute, chronic and isolation class and analyse the effects of the isolation class on the transmission dynamics of the disease. We calculate the basic reproduction number R0 and show that for R0≤1, the disease-free equilibrium is globally asymptotically stable. In addition, it is shown that for a special case when R0>1, the endemic equilibrium is locally asymptotically stable. Furthermore, an analogous stochastic epidemic model for Hepatitis C is formulated using a continuous time Markov chain. Numerical simulations are used to estimate the mean, variance and probability distributions of the discrete random variables and these are compared to the steady-state solutions of the deterministic model. Finally, the expected time to disease extinction is estimated for the stochastic model and the impact of isolation on the time to extinction is explored.  相似文献   

8.
We consider two viral strains competing against each other within individual hosts (at cellular level) and at population level (for infecting hosts) by studying two cases. In the first case, the strains do not mutate into each other. In this case, we found that each individual in the population can be infected by only one strain and that co-existence in the population is possible only when the strain that has the greater basic intracellular reproduction number, R 0c , has the smaller population number R 0p . Treatment against the one strain shifts the population equilibrium toward the other strain in a complicated way (see Appendix B). In the second case, we assume that the strain that has the greater intracellular number R 0c can mutate into the other strain. In this case, individual hosts can be simultaneously infected by both strains (co-existence within the host). Treatment shifts the prevalence of the two strains within the hosts, depending on the mortality induced by the treatment, which is, in turn, dependent upon the doses given to each individual. The relative proportions of the strains at the population level, under treatment, depend both on the relative proportions within the hosts (which is determined by the dosage of treatment) and on the number of individuals treated per unit time, that is, the rate of treatment. Implications for cases of real diseases are briefly discussed.  相似文献   

9.
We integrated soil models with an established ecosystem process model (SIPNET, simplified photosynthesis and evapotranspiration model) to investigate the influence of soil processes on modelled values of soil CO2 fluxes (R Soil). Model parameters were determined from literature values and a data assimilation routine that used a 7-year record of the net ecosystem exchange of CO2 and environmental variables collected at a high-elevation subalpine forest (the Niwot Ridge AmeriFlux site). These soil models were subsequently evaluated in how they estimated the seasonal contribution of R Soil to total ecosystem respiration (TER) and the seasonal contribution of root respiration (R Root) to R Soil. Additionally, these soil models were compared to data assimilation output of linear models of soil heterotrophic respiration. Explicit modelling of root dynamics led to better agreement with literature values of the contribution of R Soil to TER. Estimates of R Soil/TER when root dynamics were considered ranged from 0.3 to 0.6; without modelling root biomass dynamics these values were 0.1–0.3. Hence, we conclude that modelling of root biomass dynamics is critically important to model the R Soil/TER ratio correctly. When soil heterotrophic respiration was dependent on linear functions of temperature and moisture independent of soil carbon pool size, worse model-data fits were produced. Adding additional complexity to the soil pool marginally improved the model-data fit from the base model, but issues remained. The soil models were not successful in modelling R Root/R Soil. This is partially attributable to estimated turnover parameters of soil carbon pools not agreeing with expected values from literature and being poorly constrained by the parameter estimation routine. We conclude that net ecosystem exchange of CO2 alone cannot constrain specific rhizospheric and microbial components of soil respiration. Reasons for this include inability of the data assimilation routine to constrain soil parameters using ecosystem CO2 flux measurements and not considering the effect of other resource limitations (for example, nitrogen) on the microbe biomass. Future data assimilation studies with these models should include ecosystem-scale measurements of R Soil in the parameter estimation routine and experimentally determine soil model parameters not constrained by the parameter estimation routine.  相似文献   

10.
Summary The role of 4-hydroxyproline (Hyp) in stabilizing collagen triple helical structure has been investigated comprehensively. Recently it was emphasized that the preferential pyrrolidine ring pucker influenced by the stereoelectronic effects of substituted groups mainly affects the thermal stability of the triple helix. To examine this explanation, we synthesized and characterized (fPro R -Pro-Gly)10 and (fPro S -Pro-Gly)10. According to the results of CD and analytical ultracentrifugation, (fPro S -Pro-Gly)10 takes a triple helical structure and (fPro R -Pro-Gly)10 exists in a single chain structure, the trend of which is not consistent with the relationship between (Hyp S -Pro-Gly)10 and (Hyp R -Pro-Gly)10. In order to rationalize experimental results as a whole, we carried out DSC analyses and determined the thermodynamic parameters associated with the structural transition of these collagen model peptides. In this paper, we reported the DSC results for (Pro-Pro-Gly)10, (Pro-Hyp R -Gly)10 and (Pro-fPro R -Gly)10 as a part of this study. Based on those parameters, we concluded that Hyp and fPro stabilize the triple helix in different stabilizing mechanisms; the increased stability of (Pro-Hyp R -Gly)10 is ascribed primarily to the enthalpic effects while that of (Pro-fPro R -Gly)10 is achieved through the entropic ones.  相似文献   

11.
Attributable risk has become an important concept in clinical epidemiology. In this paper, we suggest to estimate the attributable risk of nosocomial infections using a multistate approach. Recently, a multistate model (called progressive disability model in the literature) has been developed in order to take into consideration both the time‐dependency of the risk factor (e.g., nosocomial infections) and the presence of competing risks (e.g., death and discharge) at each time point. However, this approach does not take into account the possible heterogeneity of the study population. In this paper, we investigate an extension of this model and suggest an adjusted disability multistate model including covariates in each transition. This new multistate model has led us to define the concepts of overall and profiled attributable risk. We use a classical semiparametric approach to estimate the model and the new attributable risk. A simulation study is investigated and we show, in particular, that neglecting the presence of covariates when estimating the model can lead to an important bias. The methodology developed in this paper is applied to data on ventilator‐associated pneumonia in 12 French intensive care units.  相似文献   

12.
In this paper we consider the phenomenon of backward bifurcation in epidemic modelling illustrated by an extended model for Bovine Respiratory Syncytial Virus (BRSV) amongst cattle. In its simplest form, backward bifurcation in epidemic models usually implies the existence of two subcritical endemic equilibria for R 0 < 1, where R 0 is the basic reproductive number, and a unique supercritical endemic equilibrium for R 0 > 1. In our three-stage extended model we find that more complex bifurcation diagrams are possible. The paper starts with a review of some of the previous work on backward bifurcation then describes our three-stage model. We give equilibrium and stability results, and also provide some biological motivation for the model being studied. It is shown that backward bifurcation can occur in the three-stage model for small b, where b is the common per capita birth and death rate. We are able to classify the possible bifurcation diagrams. Some realistic numerical examples are discussed at the end of the paper, both for b small and for larger values of b.   相似文献   

13.
The focus of this study was to empirically estimate the specific cake resistance (SCR) by the variation in shear intensity (G) in four laboratory-scale MBRs. The control reactor (MBR0) was operated with aeration only while other MBRs (MBR150, MBR300 and MBR450) were operated with aeration and mechanical mixing intensities of 150, 300 and 450 rpm, respectively. It was found that the SCR was strongly correlated (R2 = 0.99) with the fouling rates in the MBRs. Moreover, the contribution of cake resistance (Rc) to the total hydraulic resistance (Rt) was predominant compared to the irreversible fouling resistance (Rf). On this basis, the cake filtration model was selected as a predictive tool for membrane fouling. This model was modified by replacing the SCR with its empirical shear intensity relationship. The modified model can predict the fouling rate for a given shear intensity (G) within 80 and 250 s−1 in a MBR system.  相似文献   

14.
Protein kinase A (PKA) holoenzyme consists of two catalytic (C) subunits and a regulatory (R) subunit dimer (R2C2). The kinase is activated by the binding of cAMPs to the two cyclic nucleotide binding domains (CBDs), A and B, on each R-subunit. Despite extensive study, details of the allosteric mechanisms underlying the cooperativity of holoenzyme activation remain unclear. Several Markov state models of PKA-RIα were developed to test competing theories of activation for the R2C2 complex. We found that CBD-B plays an essential role in R-C interaction and promotes the release of the first C-subunit prior to the binding to CBD-A. This favors a conformational selection mechanism for release of the first C-subunit of PKA. However, the release of the second C-subunit requires all four cAMP sites to be occupied. These analyses elucidate R-C heterodimer interactions in the cooperative activation of PKA and cAMP binding and represent a new mechanistic model of R2C2 PKA-RIα activation.  相似文献   

15.
Local reflection coefficients (R) provide important insights into the influence of wave reflection on vascular haemodynamics. Using the relatively new time-domain method of wave intensity analysis, R has been calculated as the ratio of the peak intensities (RPI) or areas (RCI) of incident and reflected waves, or as the ratio of the changes in pressure caused by these waves (RΔP). While these methods have not yet been compared, it is likely that elastic non-linearities present in large arteries will lead to changes in the size of waves as they propagate and thus errors in the calculation of RPI and RCI. To test this proposition, RPI, RCI and RΔP were calculated in a non-linear computer model of a single vessel with various degrees of elastic non-linearity, determined by wave speed and pulse amplitude (ΔP+), and a terminal admittance to produce reflections. Results obtained from this model demonstrated that under linear flow conditions (i.e. as ΔP+→0), RΔP is equivalent to the square-root of RPI and RCI (denoted by RPIp and RCIp). However for non-linear flow, pressure-increasing (compression) waves undergo amplification while pressure-reducing (expansion) waves undergo attenuation as they propagate. Consequently, significant errors related to the degree of elastic non-linearity arise in RPI and RCI, and also RPIp and RCIp, with greater errors associated with larger reflections. Conversely, RΔP is unaffected by the degree of non-linearity and is thus more accurate than RPI and RCI.  相似文献   

16.
In sub-Saharan Africa, the model of care for people who are living with HIV/AIDS has changed from hospital care to home-based care. In this paper, a mathematical model describing the dynamics of HIV transmission, hospitalization, and home-based care is constructed and analysed. The model reproduction number R e is determined and discussed. The equilibria are determined and analysed in terms of R e . It is shown that if R e <1, the disease free equilibrium is both locally and globally asymptotically stable. The model has a unique endemic equilibrium and is locally asymptotically stable whenever R e >1. Five cases arise in the discussion of R e pertaining to intervention strategies. Numerical simulations are done to compare the impact of each strategy on the dynamics of HIV/AIDS. The model is fitted to the prevalence data estimates from UNAIDS on Zimbabwe. The implications of some key epidemiological parameters are investigated numerically. Projections are made to determine the possible long term trends of the prevalence of HIV in Zimbabwe.  相似文献   

17.
At elevated atmospheric CO2 concentrations ([CO2]a), photosynthetic capacity (Amax) and root fraction (ηR, the ratio of root to plant dry mass) increased in some studies and decreased in others. Here, we have explored possible causes of this, focusing on the relative magnitudes of the effects of elevated [CO2]a on specific leaf (nm) and plant (np) nitrogen concentrations, leaf mass per unit area (h), and plant nitrogen productivity (α). In our survey of 39 studies with 35 species, we found that elevated [CO2]a led to decreased nm and np in all the studies and to increased h and α in most of the studies. The magnitudes of these changes varied with species and with experimental conditions. Based on a model that integrated [CO2]a-induced changes in leaf nitrogen into a biochemically based model of leaf photosynthesis, we predicted that, to a first approximation, photosynthesis will be upregulated (Amax will increase) when growth at increased [CO2]a leads to increases in h that are larger than decreases in nm. Photosynthesis will be downregulated (Amax will decrease) when increases in h are smaller than decreases in nm. The model suggests that photosynthetic capacity increases at elevated [CO2]a only when additional leaf mesophyll more than compensates the effects of nitrogen dilution. We considered two kinds of regulatory paradigms that could lead to varying responses of ηR to elevated [CO2]a, and compared the predictions of each with the data. A simple static model based on the functional balance concept predicts that ηR should increase when neither np nor h is very responsive to elevated [CO2]a. The quantitative and qualitative agreement of the predictions with data from the literature, however, is poor. A model that predicts ηR from the relative sensitivities of photosynthesis and relative growth rate to elevated [CO2]a corresponds much more closely to the observations. In general, root fraction increases if the response of photosynthesis to [CO2]a is greater than that of relative growth rate.  相似文献   

18.
A mathematical model of burster neuron R15 from the abdominal ganglion of Aplysia is presented. This is an improvement over earlier models in that the bursting mechanism is more accurately represented. The improved model allows for simulated application of the neurotransmitter serotonin, which has been reported to have profound effects on the voltage waveform produced by R15. Computational analysis indicates that the serotonin-induced modulation of the waveform can be explained in terms of competition between stationary, bursting, and beating attractors. Analysis also indicates that, as a result of this competition, serotonin increases the sensitivity of the neuron to synaptic perturbations. This may have important consequences with regard to water balance in the Aplysia, particularly during egg laying.  相似文献   

19.
Rust is a serious fungal disease in the sunflower growing areas worldwide with increasing importance in North America in recent years. Several genes conferring resistance to rust have been identified in sunflower, but few of them have been genetically mapped and linked to molecular markers. The rust resistance gene R 4 in the germplasm line HA-R3 was derived from an Argentinean open-pollinated variety and is still one of most effective genes. The objectives of this study were to determine the chromosome location of the R 4 gene and the allelic relationship of R 4 with the R adv rust resistance gene. A total of 63 DNA markers previously mapped to linkage group (LG) 13 were used to screen for polymorphisms between two parental lines HA 89 and HA-R3. A genetic map of LG 13 was constructed with 21 markers, resulting in a total map length of 93.8 cM and an average distance of 4.5 cM between markers. Two markers, ZVG61 and ORS581, flanked the R 4 gene at 2.1 and 0.8 cM, respectively, and were located on the lower end of LG 13 within a large NBS-LRR cluster identified previously. The PCR pattern generated by primer pair ZVG61 was unique in the HA-R3 line, compared to lines HA-R1, HA-R4, and HA-R5, which carry other R 4 alleles. A SCAR marker linked to the rust resistance gene R adv mapped to LG 13 at 13.9 cM from the R 4 locus, indicating that R adv is not an allele of the R 4 locus. The markers tightly linked to the R 4 gene will facilitate gene pyramiding for rust resistance breeding of sunflower.  相似文献   

20.
This article evaluates the suitability of the ECOSSE model to estimate soil greenhouse gas (GHG) fluxes from short rotation coppice willow (SRC‐Willow), short rotation forestry (SRF‐Scots Pine) and Miscanthus after land‐use change from conventional systems (grassland and arable). We simulate heterotrophic respiration (Rh), nitrous oxide (N2O) and methane (CH4) fluxes at four paired sites in the UK and compare them to estimates of Rh derived from the ecosystem respiration estimated from eddy covariance (EC) and Rh estimated from chamber (IRGA) measurements, as well as direct measurements of N2O and CH4 fluxes. Significant association between modelled and EC‐derived Rh was found under Miscanthus, with correlation coefficient (r) ranging between 0.54 and 0.70. Association between IRGA‐derived Rh and modelled outputs was statistically significant at the Aberystwyth site (= 0.64), but not significant at the Lincolnshire site (= 0.29). At all SRC‐Willow sites, significant association was found between modelled and measurement‐derived Rh (0.44 ≤  0.77); significant error was found only for the EC‐derived Rh at the Lincolnshire site. Significant association and no significant error were also found for SRF‐Scots Pine and perennial grass. For the arable fields, the modelled CO2 correlated well just with the IRGA‐derived Rh at one site (= 0.75). No bias in the model was found at any site, regardless of the measurement type used for the model evaluation. Across all land uses, fluxes of CH4 and N2O were shown to represent a small proportion of the total GHG balance; these fluxes have been modelled adequately on a monthly time‐step. This study provides confidence in using ECOSSE for predicting the impacts of future land use on GHG balance, at site level as well as at national level.  相似文献   

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