Modeling conductive heat transfer and process uniformity during batch high-pressure processing of foods

A numerical model for predicting conductive heat transfer during batch high hydrostatic pressure (HHP) processing of foods was developed and tested for a food simulator (agar gel). For a comprehensive evaluation of the proposed method, both "conventional" HHP processes, HHP processes with gradual, step-by-step pressure buildup and pressure release, and pressure cycling HHP processes were included. In all cases, good agreement between experimental and predicted temperature profiles was observed. The model provides a very useful tool to evaluate batch HHP processes in terms of uniformity of any heat- and/or pressure-related effect. This is illustrated for inactivation of Bacillus subtilis alpha-amylase, an enzymatic model system with known pressure-temperature degradation kinetics.     

Individual-based modelling of Pinus sylvestris invasion after grazing abandonment in the French Massif Central

In the Chaîne des Puys, a mid-elevation volcanic mountain of the French Massif Central, Scots pine proves to be an invasive species colonizing abandoned lawns or heathlands, and forms in a few years monospecific natural forests. Most of the abandonment occurred 30 to 40 years ago and this process has now stopped. Thus, we lack data on the very first phase of tree colonization. We anticipate that a simulation tool could bring an appreciable help in (i) rebuilding the entire colonization process – including the initial phase – of pine settlement and (ii) answering questions about the origin of the narrow and unimodal distributions of age of pine stands we observed. In addition, such a simulator could help managers to forecast extension of Scots pine and to predict growth and evolution of present secondary forests. A spatially explicit individual-based model is presented. The model takes into account both space and time and includes growth of trees, seed production and seed dispersal, death and competition between individuals. The influence of the initial parameters are analyzed and elements of validation given. The model was then used to predict tree settlement and stand establishment using the initial conditions from a natural stand studied in the field whose characteristics before abandonment were known (number and age-distribution of trees, location of mother trees, time of abandonment). Three simulations were achieved by using the same initial conditions but following different scenarios for the recruitment process. The scenario of a fluctuating resistance of the resident vegetation (that controls the susceptibility of the environment to tree establishment) seemed as one of the most probable to explain the actual stand characteristics. We thus concluded that dynamic models could be improved by taking into account the resistance of the vegetation to colonization as a fluctuating parameter instead of a static and permanent attribute.     

Reafferent control of optomotor yaw torque inDrosophila melanogaster

Summary In the flight simulator the optomotor response ofDrosophila melanogaster does not operate as a simple feedback loop. Reafferent and exafferent motion stimuli are processed differently. Under open-loop conditions responses to motion are weaker than under closed-loop conditions. It takes the fly less than 100 ms to distinguish reafferent from exafferent motion. In closed-loop conditions, flies constantly generate torque fluctuations leading to small-angle oscillations of the panorama. This reafferent motion stimulus facilitates the response to exafferent motion but does not itself elicit optomotor responses. Reafference control appears to be directionally selective: while a displacement of the patternm by as little as 0.1° against the expected direction leads to a fast syndirectional torque response, displacements in the expected direction have no comparable effect. Based on the behavior of the mutantrol sol, which under open-loop conditions is directionally motion-blind but in closed-loop conditions still performs optomotor balance, a model is proposed in which the fly's endogenous torque fluctuations are an essential part of the course control process. It is argued that the model may also account for wild type optomotor balance in the flight simulator.     

Lessons on pattern formation from planet WATOR

It is well known that if reacting species experience unequal diffusion rates, then dynamics that lead to a constant steady state in a "well-mixed" environment can in a spatial setting lead to interesting patterns. In this paper, we focus on complementary pattern formation mechanisms that operate even when the diffusion rates are equal. In particular, we can say that when the mean-field ODE has an attracting periodic orbit then the stochastic spatial model will have large-scale spatial structures in equilibrium. We explore this mechanism in depth through the dynamics of the simulator WATOR.     

Fitting conditional survival models to meta-analytic data by using a transformation toward mixed-effects models

Summary .   Frailty models are widely used to model clustered survival data. Classical ways to fit frailty models are likelihood-based. We propose an alternative approach in which the original problem of "fitting a frailty model" is reformulated into the problem of "fitting a linear mixed model" using model transformation. We show that the transformation idea also works for multivariate proportional odds models and for multivariate additive risks models. It therefore bridges segregated methodologies as it provides a general way to fit conditional models for multivariate survival data by using mixed models methodology. To study the specific features of the proposed method we focus on frailty models. Based on a simulation study, we show that the proposed method provides a good and simple alternative for fitting frailty models for data sets with a sufficiently large number of clusters and moderate to large sample sizes within covariate-level subgroups in the clusters. The proposed method is applied to data from 27 randomized trials in advanced colorectal cancer, which are available through the Meta-Analysis Group in Cancer.     

Automatic search for model to simulate the differentiation of T lymphocytes within the thymus

The differentiation of T Lymphocytes within the thymus is an important biological phenomenon during wich these cell acquire their functions to further control the immune system. Numerous experiments under various conditions have been devised to understand the different mechanisms involved in this complex process. Nevertheless, interpretation of these experiments lead to still contradictory debatable hypotheses. Modelisation of this process through classical simulation methods cannot be envisaged because they are not adapted to modifications of the model structure, which is the point of interest. For these reasons, we proposed a new approach of automatic search for model. The program consists of four independent connected modules : The generator produces model, based on the rationale of formal grammars. Protocol and experimental data are stored in a set of experiments. The simulator using a protocol and a model provides simulated results. Finally, the supervisor by comparing simulated results and experimental data, adapts the model parameters to increase their fit and either chooses a new experiment to explore, or modifies the model structure. Change of the model structure is performed among still unexplored models according to their promise level, which is iteratively evaluated relatively to previously explored models through a proposed model distance. The generator is written in Prolog and the other modules in C++. The architecture of the program allows us to modify or complete a module without changing anything in the other modules. As a consequence, the proposed modeling approach conceived to study T lymphocyte differentiation within the thymus remains independent of this biological phenomenon and can be applied to other biological problems.     

Analysis of survival data with cross-effects of survival functions

We present a model and semiparametric estimation procedures for analysis of survival data with cross-effects (CE) of survival functions. Finite sample properties of the estimators are analyzed by simulation. A goodness-of-fit test for the proportional hazards model against the CE model is proposed. The well known data concerning effects of chemotherapy and radiotherapy on the survival times of gastric cancer patients is analyzed as an example.     

An energy dissipation and cross shear time dependent computational wear model for the analysis of polyethylene wear in total knee replacements

The cost and time efficiency of computational polyethylene wear simulations may enable the optimization of total knee replacements for the reduction of polyethylene wear. The present study proposes an energy dissipation wear model for polyethylene which considers the time dependent molecular behavior of polyethylene, aspects of tractive rolling and contact pressure. This time dependent – energy dissipation wear model was evaluated, along with several other wear models, by comparison to pin-on-disk results, knee simulator wear test results under various kinematic conditions and knee simulator wear test results that were performed following the ISO 14243-3 standard. The proposed time dependent – energy dissipation wear model resulted in improved accuracy for the prediction of pin-on-disk and knee simulator wear test results compared with several previously published wear models.     

一种新的DNA复制和转录模型

DNA复制和转录有两种模型,一种是传统的滑动模型,复制和转录发生时参与反应的蛋白质沿DNA模板滑动.在另一种新提出的工厂模型中,固定在核结构上的蛋白质拉动模板来完成DNA的复制和转录.来自生物化学、生物物理学和细胞生物学等的实验证据表明,新的工厂模型是生物活体细胞内真实的复制和转录模式.     

Forecasting with the age-period-cohort model and the extended chain-ladder model

We consider forecasting from age-period-cohort models, as wellas from the extended chain-ladder model. The parameters of thesemodels are known only to be identified up to linear trends.Forecasts from such models may therefore depend on arbitrarylinear trends. A condition for invariant forecasts is proposed.A number of standard forecast models are analysed.     

Clinical Efficacy of Simulated Vitreoretinal Surgery to Prepare Surgeons for the Upcoming Intervention in the Operating Room

Purpose

To evaluate the efficacy of the virtual reality training simulator Eyesi to prepare surgeons for performing pars plana vitrectomies and its potential to predict the surgeons’ performance.

Methods

In a preparation phase, four participating vitreoretinal surgeons performed repeated simulator training with predefined tasks. If a surgeon was assigned to perform a vitrectomy for the management of complex retinal detachment after a surgical break of at least 60 hours it was randomly decided whether a warmup training on the simulator was required (n = 9) or not (n = 12). Performance at the simulator was measured using the built-in scoring metrics. The surgical performance was determined by two blinded observers who analyzed the video-recorded interventions. One of them repeated the analysis to check for intra-observer consistency. The surgical performance of the interventions with and without simulator training was compared. In addition, for the surgeries with simulator training, the simulator performance was compared to the performance in the operating room.

Results

Comparing each surgeon’s performance with and without warmup trainingshowed a significant effect of warmup training onto the final outcome in the operating room. For the surgeries that were preceeded by the warmup procedure, the performance at the simulator was compared with the operating room performance. We found that there is a significant relation. The governing factor of low scores in the simulator were iatrogenic retinal holes, bleedings and lens damage. Surgeons who caused minor damage in the simulation also performed well in the operating room.

Conclusions

Despite the large variation of conditions, the effect of a warmup training as well as a relation between the performance at the simulator and in the operating room was found with statistical significance. Simulator training is able to serve as a warmup to increase the average performance.     

Visual control of straight flight in Drosophila melanogaster

Summary The optomotor system of Drosophila is investigated in a flight simulator in which the fly's yaw torque controls the angular velocity of the panorama (striped drum, negative feedback). Flies in the flight simulator maintain a stable orientation even in a homogeneously textured panorama without landmarks. During straight flight, torque is not zero. It consists of small pulses mostly alternating in polarity. The course is controlled by the duration (and possibly amplitude) of the pulses. The system operates under reafference control. By comparing the pulses with the visual input the system continuously measures and adjusts the efficacy of the torque output. The comparison, however, is not between angular velocity and yaw torque but, instead, between visual acceleration and pretorque, the first time derivative of torque. For comparison, the system first computes a cross-correlation. If the correlation coefficient is above a certain threshold the system calculates the external gain and adjusts its internal gain so as to keep the total gain constant. With the correlation coefficient below threshold, however, the system keeps the internal gain low despite the infinitely small external gain. We propose that for a reafferent optomotor system the coupling coefficient and the correlation coefficient of pretorque and visual acceleration are more relevant than the distinction between exafference and reafference.Abbreviation EMD elementary movement detector     

Modeling daily and subdaily cycles in rat sleep data

We developed a statistical model for rat sleep-wake behavior over the 24-hour day; this model could be used for animals exposed to shorter cycles of light and dark conditions. Rat behavior was classified either as "wake" or "sleep," as determined by analysis of electrophysiological data. The proposed model consists of three parts: the first two explain cyclic effects relating to the lighting conditions, whereas the last part reflects any acyclic effect. Hypothesis tests were conducted on the magnitude of the parts. The model also accounts for correlated errors.     

"Smooth" semiparametric regression analysis for arbitrarily censored time-to-event data

Summary .   A general framework for regression analysis of time-to-event data subject to arbitrary patterns of censoring is proposed. The approach is relevant when the analyst is willing to assume that distributions governing model components that are ordinarily left unspecified in popular semiparametric regression models, such as the baseline hazard function in the proportional hazards model, have densities satisfying mild "smoothness" conditions. Densities are approximated by a truncated series expansion that, for fixed degree of truncation, results in a "parametric" representation, which makes likelihood-based inference coupled with adaptive choice of the degree of truncation, and hence flexibility of the model, computationally and conceptually straightforward with data subject to any pattern of censoring. The formulation allows popular models, such as the proportional hazards, proportional odds, and accelerated failure time models, to be placed in a common framework; provides a principled basis for choosing among them; and renders useful extensions of the models straightforward. The utility and performance of the methods are demonstrated via simulations and by application to data from time-to-event studies.     

A New Simple Method for Improving QTL Mapping Under Selective Genotyping

The selective genotyping approach, where only individuals from the high and low extremes of the trait distribution are selected for genotyping and the remaining individuals are not genotyped, has been known as a cost-saving strategy to reduce genotyping work and can still maintain nearly equivalent efficiency to complete genotyping in QTL mapping. We propose a novel and simple statistical method based on the normal mixture model for selective genotyping when both genotyped and ungenotyped individuals are fitted in the model for QTL analysis. Compared to the existing methods, the main feature of our model is that we first provide a simple way for obtaining the distribution of QTL genotypes for the ungenotyped individuals and then use it, rather than the population distribution of QTL genotypes as in the existing methods, to fit the ungenotyped individuals in model construction. Another feature is that the proposed method is developed on the basis of a multiple-QTL model and has a simple estimation procedure similar to that for complete genotyping. As a result, the proposed method has the ability to provide better QTL resolution, analyze QTL epistasis, and tackle multiple QTL problem under selective genotyping. In addition, a truncated normal mixture model based on a multiple-QTL model is developed when only the genotyped individuals are considered in the analysis, so that the two different types of models can be compared and investigated in selective genotyping. The issue in determining threshold values for selective genotyping in QTL mapping is also discussed. Simulation studies are performed to evaluate the proposed methods, compare the different models, and study the QTL mapping properties in selective genotyping. The results show that the proposed method can provide greater QTL detection power and facilitate QTL mapping for selective genotyping. Also, selective genotyping using larger genotyping proportions may provide roughly equivalent power to complete genotyping and that using smaller genotyping proportions has difficulties doing so. The R code of our proposed method is available on http://www.stat.sinica.edu.tw/chkao/.     

The SBML discrete stochastic models test suite

MOTIVATION: Stochastic simulation is a very important tool for mathematical modelling. However, it is difficult to check the correctness of a stochastic simulator, since any two realizations from a single model will typically be different. RESULTS: We have developed a test suite of stochastic models that have been solved either analytically or using numerical methods. This allows the accuracy of stochastic simulators to be tested against known results. The test suite is already being used by a number of stochastic simulator developers. AVAILABILITY: The latest version of the test suite can be obtained from http://www.calibayes.ncl.ac.uk/Resources/dsmts/ and is licensed under GNU Lesser General Public License.     

A methodology for risk analysis of plurivorous fungi in biological weed control: Sclerotinia sclerotiorum as a model

In New Zealand, research is being performed on the use of the ubiquitous plurivorous ascomycete Sclerotinia sclerotiorum, as a biocontrol agent for Cirsium arvense in pasture. As a consequence of the wide host range of this fungus, the proposed biocontrol may pose a risk to non-target arable plants. Crop disease risk is primarily due to the formation of sclerotia. These perennating bodies may directly infect susceptible crops sown at the biocontrol site in years after the biocontrol event. Additionally they may cause infection in neighbouring crops through the formation of apothecia from which airborne ascospores are dispersed. A methodology for a risk analysis is proposed, embodying both temporal and spatial processes, where the relative disease risk from biocontrol is defined as the ratio of added to naturally occurring inoculum.Exponential decay is proposed as a suitable model for the survival of sclerotia in soils beneath pastures, and data from an ongoing study are used in a preliminary parameterisation. The model is applied to published data on initial sclerotium population size and unpublished data on natural levels of soilborne sclerotia, to reveal how a withholding period, defined as the interval of time that must elapse for the ratio of added to natural inoculum to equal unity, may be calculated.For quantifying escape and aerial dispersal of ascospores from a treated pasture, three mechanistic models are proposed. Firstly, a simple one-layer model of escape, giving a provisional estimation of 81% of released ascospores escaping the pasture canopy, is discussed. Secondly, ascospore dispersal within and close to the biocontrol site (<30 m) is described by a model revealing abrupt decline in the atmospheric concentration of ascospores within short distances from the biocontrol site. Thirdly, for predicting ascospore concentrations at greater distances (>100 m), a Gaussian plume model is proposed. In a first approximation, these models are used in an example calculation to show how a hypothetical safety zone might be determined. A map of the province of Canterbury showing the locations of different agricultural activities and infestations of dense populations of C. arvense, revealed that potential biocontrol sites mostly do not border arable land and that a safety zone would therefore be feasible.The study presented here provides conceptual and mathematical frameworks for risk analysis of the use of plurivorous fungi in biological weed control, using S. sclerotiorum as an example. However, before a judgement may be made about the phytosanitory risks associated with the use of S. sclerotiorum to control C. arvense in pastures in Canterbury, the models developed in this paper must be parameterized using data collected under a wide range of conditions in the field.     

作物水分供应订正函数的韦伯函数型

从作物水分生产潜力、潜在水分利用效率与水分满足率的关系及特点入手,引入水分供应订正函数的韦伯形式。与目前常见的水分供应订正函数形式相比,本文给出的韦伯形式的水分供应订正函数具有临界水分满足率和“旋回”特征,能较好地解释作物水分生产潜力与水分满足率之间的数量关系,模型的实用性较广。模型中位置参数表示临界水分满足率;尺度参数表示水分满足率的取值范围;形状参数决定水分供应订正函数的“峰度”和“偏斜度”。根据“图解法”可求取水分供应订正函数的相关参数。其参数也具有明确的生物学和物理学意义,参数值本身也较稳定,使模型在应用中可望具有良好的稳定性。     

Structure modeling of the acetylcholine receptor channel and related ligand gated channels

In this model-building study a model for the pore of the acetylcholine receptor channel is proposed. The pore is formed by five -helices of the M2 segment where three rings of hydrophilic side chains point into the channel lumen. This model is in agreement with most experimental data like photolabeling, drug affinity studies, single channel conductivity measurements and cryo electron microscopy known about this channel.This study predicts a strong coupling of the motion of the ions in the channel to that of the charged and highly hydrophilic amino acid side chains at the channel wall. Due to the negative net-charge in the pore more than a single cation may occupy the pore region. The resulting strong local electric fields make the commonly used constant field approximation obsolete for this type of ion channel.