Heterogeneity of the digestible insoluble fiber of selected forages in situ

Long-term in situ incubations were performed to verify the likelihood of the heterogeneity concept of the potentially digestible fraction of the insoluble fiber (NDFom) by fitting both heterogeneous and homogeneous potentially digestible NDFom versions of a generalized compartmental model of digestion (GCMD). Corn silage and eleven tropical grasses and alfalfa hay were studied. Data were gathered from a study in which forage samples in nylon bags were incubated in rumen cannulated steers so that three profiles per forage were generated. The incubation endpoint was used to form sets of time profiles. The original set consisted of profiles ending at 1440 h, and the other two were formed by using 96 and 240 h as the incubation endpoints, respectively. The indigestible residue was estimated using nonlinear least squares or by assuming it to be 2.4 times lignin determined by the sulphuric acid method (Lignin (sa)). Therefore, eight different models were evaluated by combining end points of digestion, and the homogeneous and heterogeneous versions of GCMD with the two ways of estimating the indigestible residue. The likelihood of the models was assessed by computing Akaike information criteria. The effects of forage, model, and their interaction were analyzed by taking model as a repeated measurement. Heterogeneity of the potentially degradable fraction for NDFom was detected with long-term incubation trials (up to 1440 h) for some forages, and the introduction of the 2.4×Lignin (sa) as a direct measure of the indigestible residue improved the likelihood of the heterogeneous version of GCMD. The forage by model interaction was significant for many comparable parameter estimates, which means that specific and inconsistent results for models within forages were produced depending on the definition of the incubation end-point. The indigestible residue was overestimated with short-term incubation profiles, but the overestimation was lower for the profiles ending at 240 h whether compared to profiles ending at 96 h. Given the likelihood of the heterogeneous version of GCMD fitted to profiles ending at 1440 h and at 240 h for some forages, the heterogeneity concept should be investigated whenever the research interest relies on estimating the kinetic attributes of the degradation profiles of the NDFom in situ.     

Effects of hybrid and maturity on performance and nutritive characteristics of forage maize at high latitudes, estimated using the gas production technique

We evaluated effects of hybrid and advancing plant maturity on performance, chemical composition, and nutritional characteristics of whole plant forage maize as well as the relative contributions of its plant fractions at high latitudes. Three maize hybrids, Avenir (FAO 180), Isberi (FAO 190) and Burli (FAO 210), were grown in southern Sweden in a field experiment with a replicated complete randomized block design. Plants were harvested four times during maturation, and dry matter (DM) yield and DM as a proportion of fresh weight were recorded. Whole plants were separated into four morphological fractions representing stems, leaves, kernels and cobs and the contribution of each fraction to the DM of the whole plant was estimated. Plant material was subjected to chemical analysis followed by measurement of in vitro gas production (GP) in buffered rumen fluid and finally, by calculation of in vitro true digestibility of organic matter (OM) and neutral detergent fibre (aNDFom). The GP profiles were fitted to a first order kinetic model with a discrete lag. Parameters describing the GP profiles were used in a recently developed mechanistic two compartment rumen degradation model to estimate in vivo OM digestibility (OMD) and first order rate of degradation in the rumen. Hybrids were compared and effects of maturity were assessed by analysis of variance using DM concentration as covariate. There were differences (P<0.05) among the hybrids in DM yield and relative contributions of the plant fractions. Differences (P<0.05) in modelled in vivo digestibility of OM and rates of degradation also occurred among hybrids. Increased maturity caused a reduction in in vitro digestibility of aNDFom in all plant fractions (P<0.05), but increased the rate of rumen degradation of OM in the whole plant as evaluated from GP results. The DM yield had a quadratic relationship with increasing maturity, with maximum yield at a DM concentration of about 370 g/kg. In vitro GP can describe the nutritive characteristics of forage maize in relation to advancing maturity and increased maturity affected agronomic performance and plant composition as well as the nutritive characteristics of hybrids.     

Use of the beta-binomial distribution in dominant-lethal testing for "weak mutagenic activity".

When the results of biological experiments are tested statistically for a possible difference between a treatment and its control, the statistical inferences are valid only if the statistical procedure is derived from a model that fits the experimental results satisfactorily. In this paper it is shown that a beta-binomial distribution provided a better fit than a binomial distribution when the data used were based on a large number of counts of dead and total implants on dominant-lethal tests on mice. This suggests that the probability P that an implant will die is not constant over the experimental units. Tests derived from the beta-biomial distribution have been used and their results compared with those of the tests based on the binomial or constant P assumption. The tests based on the binomial model are erroneously too severe when P is not constant in a group. The problem of knowing whether the males or the females should be considered as the experimental units is considered. In this paper, calculations are carried out for the two situations. This problem will be further studied by computer simulation and the result will be presented in a next paper.It is also shown that a negative binomial distribution could be fitted to the dead implant counts. No test based on this model was used because it ignores the total implants. No familiar distribution could be fitted to the total implant counts.     

Modified version of ADM1 model for agro-waste application

Agro-residues account for a large proportion of the wastes generated around the world. There is thus a need for a model to simulate the anaerobic digestion processes used in their treatment. We have developed model based on ADM1, to be applied to agro-wastes. We examined and tested the biodegradability of apple, pear, orange, rape, sunflower, pig manure and glycerol wastes to be used as the basis for feeding the model. Moreover, the fractions of particulate COD (X_c) were calculated, and the disintegration constant was obtained from biodegradability profiles, considering disintegration to be the limiting process. The other kinetic and stoichiometric parameters were taken from the ADM1 model.     

Biodegradation of pyrene by Mycobacterium frederiksbergense in a two-phase partitioning bioreactor system

Biodegradation of pyrene by Mycobacterium frederiksbergense was studied in a two-phase partitioning bioreactor (TPPB) using silicone oil as non-aqueous phase liquid (NAPL). The TPPB achieved complete biodegradation of pyrene; and during the active degradation phase, utilization rates of 270, 230, 139, 82 mg l(-1)d(-1) for initial pyrene loading concentrations (in NAPL) of 1000, 600, 400 and 200 mg l(-1), respectively, were obtained. The degradation rates achieved using M. frederiksbergense in TPPB were much higher than the literature reported values for an ex situ PAH biodegradation system operated using single and pure microbial species. The degradation data was fitted to simple Monod, logistic, logarithmic, three-half-order kinetic models. Among these models, only exponential growth form of the three-half-order kinetic model provided the best fit to the entire degradation profiles with coefficient of determination (R2) value >0.99. From the experimental findings, uptake of pyrene by the microorganism in TPPB was proposed to be a non-interfacial based mechanism.     

Characterization of human crossover interference

We present an analysis of crossover interference over the entire human genome, on the basis of genotype data from more than 8,000 polymorphisms in eight CEPH families. Overwhelming evidence was found for strong positive crossover interference, with average strength lying between the levels of interference implied by the Kosambi and Carter-Falconer map functions. Five mathematical models of interference were evaluated: the gamma model and four versions of the count-location model. The gamma model fit the data far better than did any of the other four models. Analysis of intercrossover distances was greatly superior to the analysis of crossover counts, in both demonstrating interference and distinguishing between the five models. In contrast to earlier suggestions, interference was found to continue uninterrupted across the centromeres. No convincing differences in the levels of interference were found between the sexes or among chromosomes; however, we did detect possible individual variation in interference among the eight mothers. Finally, we present an equation that provides the probability of the occurrence of a double crossover between two nonrecombinant, informative polymorphisms.     

Kinetics and mechanism of methylene blue sorption onto palm kernel fibre

The kinetics and mechanism of the sorptive removal of methylene blue dye from aqueous solution using palm kernel fibre as adsorbent have been investigated. Batch kinetic experiments were performed and system variables investigated includes pH and initial dye concentration. The kinetic data were fitted to the pseudo-first, pseudo-second, intraparticle diffusion and mass transfer models. The pseudo-first order reaction kinetics fitted to the experimental data only in the first 5 min of sorption and then deviated, while the pseudo-second order kinetic model was found to fit the experimental data for the entire sorption period with high coefficient of determination. Equations were developed using the pseudo-second order model, which predicts the amounts of methylene blue at any contact time and initial concentration within the given range. This suggests that the sorption of methylene blue onto palm kernel fibre follows a chemical activation mechanism. A mathematical relationship was also drawn between the equilibrium sorption capacity and the change in pH (ΔH⁺) at the end of the kinetic experiments with varying initial dye concentration, supporting the fact that chemical reaction (ion exchange) occurred and is important in the rate determining step. Mass transfer was found to be favoured at high concentrations while intraparticle diffusion was favoured at low concentrations.     

On the distribution of fast-phase intervals in optokinetic and vestibular nystagmus

 Histograms of fast-phase intervals in human optokinetic and vestibular nystagmus were generated, and fitted to statistical distributions used in previous studies. The distributions did not depend on stimulation type (optokinetic or vestibular). An inverse Gaussian or a gamma distribution fitted the data better than did a reciprocal Gaussian distribution, but none fitted the data especially well. In some cases, however, the interpretation of these distributions is more physiologically satisfactory than in others. Recommendations are made on which class of models is preferred, and the experiments needed to support the particular models. Our results call into question the validity of previous studies that fit statistical distributions to data sets of a size comparable to ours. Received: 26 June 2001 / Accepted in revised form: 20 February 2002     

Dealing with the Phenomenon of Quasi-complete Separation and a Goodness of Fit Test in Logistic Regression Models in the Case of Long Data Sets

The phenomenon of quasi-complete separation that appears in the identification of the neuromuscular system called muscle spindle by a logistic regression model is considered. The system responds when it is affected by a number of stimuli. Both the response and the stimuli are very long binary sequences of events. In the logistic model, three functions are of special interest: the threshold, the recovery and the summation functions. The maximum likelihood estimates are obtained efficiently and very fast by using the penalized likelihood function. A validity test for the fitted model based on the randomized quantile residuals is proposed. The validity test is transformed to a goodness of fit test and the use of Q–Q plot is also discussed.

     

A General and Dynamic Species Abundance Model, Embracing the Lognormal and the Gamma Models

One aspect of community ecology that has been given particular attention is the pattern of species abundances in a community. The species may have a wide range of abundances; some are very common and others rare. When species abundance models are fitted to observations, the lognormal model and one of the gamma models (e.g., the log-series model) are usually applied. The model that gives the best fit according to some goodness-of-fit test is then chosen. By applying a diffusion approximation for each species' dynamics with density regulation of the straight theta-logistic type, we here present a general species abundance model that embraces the two most widely applied species abundance models, the lognormal and the gamma. Our general model will, therefore, provide a better fit than the two special cases, except when it corresponds to one of them. In contrast to the classical models, ours is also dynamic, making it possible to evaluate the fluctuations in species abundance over time through both biotic and abiotic factors. The model is fitted to several species abundance data sets and our results compared to previous attempts to fit a model, usually either the lognormal or the log-series.     

Estimation of multivariate frailty models using penalized partial likelihood

There exists a growing literature on the estimation of gamma distributed multiplicative shared frailty models. There is, however, often a need to model more complicated frailty structures, but attempts to extend gamma frailties run into complications. Motivated by hip replacement data with a more complicated dependence structure, we propose a model based on multiplicative frailties with a multivariate log-normal joint distribution. We give a justification and an estimation procedure for this generally structured frailty model, which is a generalization of the one presented by McGilchrist (1993, Biometrics 49, 221-225). The estimation is based on Laplace approximation of the likelihood function. This leads to estimating equations based on a penalized fixed effects partial likelihood, where the marginal distribution of the frailty terms determines the penalty term. The tuning parameters of the penalty function, i.e., the frailty variances, are estimated by maximizing an approximate profile likelihood. The performance of the approximation is evaluated by simulation, and the frailty model is fitted to the hip replacement data.     

Neutrophil elastase cleaves laminin-332 (laminin-5) generating peptides that are chemotactic for neutrophils

Proteolytic processing of laminin-332 by matrix metalloproteinase (MMP)-2 and MMP-14 has been shown to yield fragments that are promigratory for epithelial cells. During acute and chronic inflammation, proteases are elaborated by neutrophils and macrophages that can degrade basement membranes. We investigated the susceptibility of laminin-332 to degradation by the following neutrophil and macrophage proteases: neutrophil elastase (NE), cathepsin G, proteinase-3, and MMPs-2, -8, -9, and -12. Protease-specific differences were seen in the capacity to cleave the individual chains of laminin-332. NE and MMP-12 showed the greatest activity toward the gamma2 chain, generating a fragment similar in size to the gamma2x fragment generated by MMP-2. The digestion pattern of laminin-332 by degranulated neutrophils was nearly identical to that generated with NE alone. Digestion by supernatants of degranulated neutrophils was blocked by an inhibitor of NE, and NE-deficient neutrophils were essentially unable to digest laminin-332, suggesting that NE is the major neutrophil-derived protease that degrades laminin-332. In vivo, laminin gamma2 fragments were found in the bronchoalveolar lavage fluid of wild-type mice treated with lipopolysaccharide, whereas that obtained from NE-deficient mice showed a different cleavage pattern. In addition, NE cleaved a synthetic peptide derived from the region of human laminin gamma2 containing the MMP-2 cleavage site, suggesting that NE may generate laminin-332 fragments that are also promigratory. Both laminin-332 fragments generated by NE digestion and NE-digested laminin gamma2 peptide were found to be chemotactic for neutrophils. Collectively, these data suggest that degradation of laminin-332 by NE generates fragments with important biological activities.     

Modeling the in vitro 20S proteasome activity: the effect of PA28-alphabeta and of the sequence and length of polypeptides on the degradation kinetics

Proteasomes are fundamental for the degradation of intracellular proteins, having a key role in several important metabolic and signaling pathways, in the cell cycle and in antigen presentation. In vitro proteasomal digestion assays are widely used in molecular biology and immunology. We developed a model, ProteaMAlg (proteasome modeling algorithm) that describes the kinetics of specific protein fragments generated by 20S proteasomes in different conditions, once the substrate cleavage strengths are provided. ProteaMAlg was tested on a variety of data available in the literature as well as on new degradation experiments performed with polypeptides of different sequences and lengths. The comparison between in vitro and in silico experiments was used to quantify the effect on degradation of the sequence and the length of target polypeptides, of the presence of regulatory molecules such as PA28-αβ, and of the type of 20S proteasome (constitutive- or immunoproteasome). The model showed that the effect of the PA28 regulatory subunit results in a modification of the gating functions of the proteasome core particle. Immunoproteasome digestion experiments suggested that this form of proteasome, which is involved in generating MHC-class I epitopes, presents modified cleavage and gating activities. Our analysis improves the current understanding of the kinetics of proteasome functioning, and provides a tool to quantify and predict the effect of key parameters during in vitro digestion. ProteaMAlg is publicly available on the web (http://www.proteamalg.com).     

Genetic noise control via protein oligomerization

Background

Biochemical equilibria are usually modeled iteratively: given one or a few fitted models, if there is a lack of fit or over fitting, a new model with additional or fewer parameters is then fitted, and the process is repeated. The problem with this approach is that different analysts can propose and select different models and thus extract different binding parameter estimates from the same data. An alternative is to first generate a comprehensive standardized list of plausible models, and to then fit them exhaustively, or semi-exhaustively.

Results

A framework is presented in which equilibriums are modeled as pairs (g, h) where g = 0 maps total reactant concentrations (system inputs) into free reactant concentrations (system states) which h then maps into expected values of measurements (system outputs). By letting dissociation constants K _d be either freely estimated, infinity, zero, or equal to other K _d , and by letting undamaged protein fractions be either freely estimated or 1, many g models are formed. A standard space of g models for ligand-induced protein dimerization equilibria is given. Coupled to an h model, the resulting (g, h) were fitted to dTTP induced R1 dimerization data (R1 is the large subunit of ribonucleotide reductase). Models with the fewest parameters were fitted first. Thereafter, upon fitting a batch, the next batch of models (with one more parameter) was fitted only if the current batch yielded a model that was better (based on the Akaike Information Criterion) than the best model in the previous batch (with one less parameter). Within batches models were fitted in parallel. This semi-exhaustive approach yielded the same best models as an exhaustive model space fit, but in approximately one-fifth the time.

Conclusion

Comprehensive model space based biochemical equilibrium model selection methods are realizable. Their significance to systems biology as mappings of data into mathematical models warrants their development.     

A validated model of passive muscle in compression

A better characterisation of soft tissues is required to improve the accuracy of human body models used, amongst other applications, for virtual crash modelling. This paper presents a theoretical model and the results of an experimental procedure to characterise the quasi-static, compressive behaviour of skeletal muscle in three dimensions. Uniaxial, unconstrained compression experiments have been conducted on aged and fresh animal muscle samples oriented at various angles from the fibre direction. A transversely isotropic hyperelastic model and a model using the theory of transverse isotropy and strain dependent Young's moduli (SYM) have been fitted to the experimental data. Results show that the hyperelastic model does not adequately fit the data in all directions of testing. In contrast, the SYM gives a good fit to the experimental data in both the fibre and cross-fibre direction, up to 30% strain for aged samples. The model also yields good prediction of muscle behaviour at 45° from the fibre direction. Fresh samples show a different behaviour than aged tissues at 45° from the fibre direction. However, the SYM is able to capture this difference and gives a good fit to the experimental data in the fibre, the cross-fibre and at 45° from the fibre direction. The model also yields good prediction of muscle behaviour when compressed at 30° and 60° from the fibre direction. The effect of the time of test after death has also been investigated. Significant stiffening of muscle behaviour is noted a few hours after death of the subject.     

Migration timing and distance from shore of southbound eastern Pacific gray whales (Eschrichtius robustus) off Ensenada,Baja California,Mexico

Eastern Pacific gray whales were monitored off Ensenada, Mexico, during the southbound migration. The objectives were to determine southbound migration timing and width of the migration corridor during three seasons (2003–2006). Migration timing was determined by fitting a generalized additive model to the shore counts for each season and estimating the 10, 50, and 90 percentiles of the fitted curves. To estimate abundance from shore‐based counts, a probability density function for the shore based distances was estimated by a product of a gamma distribution fit to the boat survey distance data for 2006/2007 and a half‐normal detection function using combined data of the three seasons. The parameters of the gamma distribution were corrected to account for less boat survey effort carried out 20–40 km than 0–20 km from shore. The onset of the migration off Ensenada was in late December/early January and ended around 13 February. The median date was 23–26 January for the first and third season and a week early for the second season. Boat surveys indicated a wide (20 km) migration corridor but most gray whales traveled within 9.9 km from shore. The estimated total number of whales during watch hours was 2,298 (95% CI = 1,536–4,447).     

真菌深层培养过程的房室结构神经网络模型

在对横纹黑蛋巢菌深层培养过程进行分析的基础上,提出一种房室结构的神经网络模型,利用ＲＢＦ网络这各房室的输入,输出关系,并进一步对整个生化过程作了建模型研究,计算结果表明,所建模型性能较佳,对真菌培养过程的观测数据拟合结果令人满意。     

Prediction of distal radius fracture in children, using a biomechanical impact model and case-control data on playground free falls

OBJECTIVES: To assess the ability of a biomechanical impact model to predict the likelihood of distal radius fracture in children using data gathered for a previous epidemiological case-control study of falls from playground equipment. METHODOLOGY: Factor of Risk (FR) values were generated for each of selected subjects from the case-control study using a biomechanical model. Logistic regression curves were fitted to examine the relationship between the FR values and the probability of radius fracture. RESULTS: Forty-five cases and thirty-one controls were selected. The logistic regression analyses showed a significant association between the probability of fracture and FR. CONCLUSIONS: The biomechanical model distinguished between children who fractured their distal radius and those who did not. The model can be used to test how risk factors, such as fall height and ground surface type, affect physical stresses transmitted through the arm and their relation to the fracture tolerance of the distal radius.