Growth Rate Regulation and Random Transition A study performed on embryonal carcinoma cell lines. I.

Abstract. Analyses of cell-cycle characteristics of the three embryonal carcinoma (EC) cell lines F9, PCC3 N/1 and PCC4 Azal, have been performed. the three lines reflect successive stages in early mouse embryogenesis as regards cell surface antigens and cell-cycle characteristics. In an attempt to understand changes in cell-cycle characteristics occurring during early embryogenesis, the two-random transition probability (TP) model was applied to the EC-cell system—and particularly to the F9 line. By utilizing an intraclonal heterogeneity in intermitotic times found in these EC lines, a growth-regulating point was introduced as a modification of the two-random TP model. the modified model was found to be very useful when demonstrating the cell-cycle growth kinetics of the F9 line. the model is used in an accompanying paper to extend the analysis of cell-cycle characteristics in undifferentiated EC cells.     

Growth rate regulation and random transition. A study performed on embryonal carcinoma cell lines. I

Analyses of cell-cycle characteristics of the three embryonal carcinoma (EC) cell lines F9, PCC3 N/1 and PCC4 Azal, have been performed. The three lines reflect successive stages in early mouse embryogenesis as regards cell surface antigens and cell-cycle characteristics. In an attempt to understand changes in cell-cycle characteristics occurring during early embryogenesis, the two-random transition probability (TP) model was applied to the EC-cell system--and particularly to the F9 line. By utilizing an intraclonal heterogeneity in intermitotic times found in these EC lines, a growth-regulating point was introduced as a modification of the two-random TP model. The modified model was found to be very useful when demonstrating the cell-cycle growth kinetics of the F9 line. The model is used in an accompanying paper to extend the analysis of cell-cycle characteristics in undifferentiated EC cells.     

人大肠癌鸡胚尿囊膜移植模型的建立及血管生成特征的观察

目的研究人大肠癌腺癌细胞株HT-29鸡胚尿囊膜移植模型建立的方法,观察和分析其血管生成的特征。方法将不同浓度的人大肠癌腺癌细胞株HT-29接种于鸡胚尿囊膜（chick embryo chorioallantoic membrane,CAM）,观察影响大肠癌鸡胚移植模型瘤体成活的因素、瘤体生长特征和血管生成情况。结果建立了人大肠癌CAM移植模型。移植模型瘤体易于生长,具有较强的血管生成作用。结论该模型易于复制,能动态观察大肠癌的血管生成过程,可用于大肠癌的生物学行为、药物筛选等领域的研究。     

Response characteristics of the BVP neuron model to periodic pulse inputs.

The characteristics of the BVP neuron model response to periodic pulse stimuli are investigated. Temporal patterns of the output of the model are analyzed as a function of the stimulus intensity and period. The BVP model exhibits the same chaotic behavior, and a Cantor function-like graph of the response frequency (mean firing rate) as in electrophysiological experiments. This shows that the BVP model describes the complicated response characteristics of the neuron at least qualitatively.     

The epitheliome: agent-based modelling of the social behaviour of cells

We have developed a new computational modelling paradigm for predicting the emergent behaviour resulting from the interaction of cells in epithelial tissue. As proof-of-concept, an agent-based model, in which there is a one-to-one correspondence between biological cells and software agents, has been coupled to a simple physical model. Behaviour of the computational model is compared with the growth characteristics of epithelial cells in monolayer culture, using growth media with low and physiological calcium concentrations. Results show a qualitative fit between the growth characteristics produced by the simulation and the in vitro cell models.     

Analysis of the plant architecture via tree-structured statistical models: the hidden Markov tree models

Plant architecture is the result of repetitions that occur through growth and branching processes. During plant ontogeny, changes in the morphological characteristics of plant entities are interpreted as the indirect translation of different physiological states of the meristems. Thus connected entities can exhibit either similar or very contrasted characteristics. We propose a statistical model to reveal and characterize homogeneous zones and transitions between zones within tree-structured data: the hidden Markov tree (HMT) model. This model leads to a clustering of the entities into classes sharing the same 'hidden state'. The application of the HMT model to two plant sets (apple trees and bush willows), measured at annual shoot scale, highlights ordered states defined by different morphological characteristics. The model provides a synthetic overview of state locations, pointing out homogeneous zones or ruptures. It also illustrates where within branching structures, and when during plant ontogeny, morphological changes occur. However, the labelling exhibits some patterns that cannot be described by the model parameters. Some of these limitations are addressed by two alternative HMT families.     

Realization of biophysical models of cardiac electrical activity

Considered are the principles of realization of biophysical models of heart ventricle electrical activity in the form of a double electric layer on the surface of the electrically active myocardium (epicardium and endocardium) and the boundary surfaces dividing the model compartments with different electrophysiological characteristics. The model parameters are the electrophysiological and anatomical characteristics of the heart such as the geometry of the ventricles and the specialized His-Purkinje conduction system, the velocity of depolarization spread over myocardium, the ratio of the velocities of excitation transmission through the Myocardium / His / Purkinje elements of the model, the shape of transmembrane action potentials on the boundary surfaces, the orientation of the intrinsic anatomical axes of the heart relative to the initial set of coordinates, and some other biophysical characteristics of the myocardium. This model is the main unit of a computer simulation system, which includes databases of real and simulated electrocardiosignals.     

On the Statistical Inference from Survival Experiments with Two Types of Failure

Formulated in terms of latent failure times a survival model with two dependent competing risks is considered. Using this model, it is possible to introduce the probabilistic characteristics of each type of failure contribution to the joint effect of two damaging agents. Confidence bounds for such characteristics are given.     

Modeling of technical training of discus throwers in the period of significant changes of their mass-inertia characteristics

The use of artificial neural networks for simulation of the control of an anthropomorphic mechanism when its mass-inertia characteristics are changing is considered in this paper. It is shown in theory that the change in mass-inertia characteristics of the model does not have a linear relationship with the output parameter but a spurt-like change in the pattern of the output function after a certain threshold. The data of the model experiment served as a basis for a full-scale test with discus throwers who had different height-weight parameters during a year of study. Specific traits in the technique of standing discus throwing are shown, and their dependence on the changes of anthropometric characteristics of sportsmen.     

大鼠糖尿病溃疡动物模型的初步研究

目的构建大鼠糖尿病溃疡动物模型,观察评价该模型的临床及病理特点。方法利用磁片循环压迫的方法,构建大鼠糖尿病溃疡动物模型,并从整体,组织和生化三个层次对糖尿病溃疡进行了研究。结果构建出了一个可以复制的糖尿病溃疡动物模型,该模型具有组织坏死、白细胞聚集以及高浓度晚期糖化终末产物等特征。结论利用缺血再灌注法构建了大鼠糖尿病溃疡动物模型。其病理改变与人极为相似,是一种很好的用于糖尿病溃疡发病机制和治疗研究的动物模型。     

A model of technical variation of microarray signals.

We describe a mathematical model of signal from single-channel direct hybridization microarray platforms. The model establishes a linear relationship between microarray signals and their standard deviations from a minimum set of assumptions. We use the model to precisely define important microarray quality characteristics: resolved fold change and dynamic range. The definitions lead to closed form expressions relating these characteristics to physical parameters of the microarray experiment in the case when both specific and nonspecific binding of target to probe are governed by the Langmuir hybridization isotherm. The predictions of the model are in close agreement to data obtained from spike-in experiments. Given the generality of the model, the introduced definitions of dynamic range and resolved concentration fold-change can be used to conduct cross-platform comparisons and to guide improvement of the microarray platform.     

Study on dynamic characteristics’ change of hippocampal neuron reduced models caused by the Alzheimer’s disease

In the paper, based on the electrophysiological experimental data, the Hippocampal neuron reduced model under the pathology condition of Alzheimer’s disease (AD) has been built by modifying parameters’ values. The reduced neuron model’s dynamic characteristics under effect of AD are comparatively studied. Under direct current stimulation, compared with the normal neuron model, the AD neuron model’s dynamic characteristics have obviously been changed. The neuron model under the AD condition undergoes supercritical Andronov–Hopf bifurcation from the rest state to the continuous discharge state. It is different from the neuron model under the normal condition, which undergoes saddle-node bifurcation. So, the neuron model changes into a resonator with monostable state from an integrator with bistable state under AD’s action. The research reveals the neuron model’s dynamic characteristics’ changing under effect of AD, and provides some theoretic basis for AD research by neurodynamics theory.     

A mathematical model of flow through a collapsible tube--I. Model and steady flow results

A one-dimensional model is presented to describe the flow through a collapsible tube whose ends are tethered to rigid tubes and which is enclosed in a pressurized chamber. Results are presented for the special case of steady flow. Predicted pressure drop versus flow rate (delta P-Q) characteristics agree qualitatively with available experimental data. The significance of the model and of various physical parameters, in regard to the shape of these characteristics, is discussed.     

Consecutive immobilized enzymatic reactions in continuous stirred tank reactor systems

The performance characteristics of two-enzyme reaction in a continuous stirred tank reactor (CSTR) are analytical investigated in this work. A model is formulated to describe the substrate concentration variations by taking into account the external and internal diffusion resistances. It is found that the reaction system exhibits the characteristics of reaction control or diffusion control depending on the operating conditions. The single CSTR model is also extended to describe the multiple CSTR system. The latter model enables the prediction of the number of CSTRs in series required to achieve a prescribed substrate conversion.     

Analysis of feedback loops and robustness in network evolution based on Boolean models

Background  

Many biological networks such as protein-protein interaction networks, signaling networks, and metabolic networks have topological characteristics of a scale-free degree distribution. Preferential attachment has been considered as the most plausible evolutionary growth model to explain this topological property. Although various studies have been undertaken to investigate the structural characteristics of a network obtained using this growth model, its dynamical characteristics have received relatively less attention.     

Prediction of replication origins by calculating DNA structural properties

In this study, we introduced two DNA structural characteristics, namely, bendability and hydroxyl radical cleavage intensity to analyze origin of replication (ORI) in the Saccharomyces cerevisiae genome. We found that both DNA bendability and cleavage intensity in core replication regions were significantly lower than in the linker regions. By using these two DNA structural characteristics, we developed a computational model for ORI prediction and evaluated the model in a benchmark dataset. The predictive performance of the jackknife cross-validation indicates that DNA bendability and cleavage intensity have the ability to describe core replication regions and our model is effective in ORI prediction.     

Identification of sound-localization cues in the HRTF of the bat-head model

Animals such as bats and dolphins exhibit impressive echolocation abilities in terms of ranging, resolution and imaging and therefore represent a valuable learning model for the study of spatial hearing and sound source localization leading to a better understanding of the hearing mechanism and further improvement of the existing localization strategies. This study aims to examine and understand the directional characteristics of a sonar receiver modeled upon the bat auditory system via measurements of the head-related transfer function (HRTF) in the horizontal plane. Four different models of the bat head were considered here and used to evaluate acoustic spectral characteristics of the sound received by the bat's ears – a sphere model, a sphere model with a pinna attached (two pinnae of different size were used in this study) and a bat-head cast. The performed HRTF measurements of the bat-head models were further analyzed and compared to identify monaural spectral localization cues in the horizontal plane defined by the bat's head and pinna shape and size. Our study suggests that the acoustical characteristics of a bio-inspired sonar head measured and specified in advance can potentially improve the performance of a receiver. Moreover, the generated auditory models may hold clues for the design of receiver characteristics in ultrasound imaging and navigation systems.     

Stream ecosystem responses to spatially variable land cover: an empirically based model for developing riparian restoration strategies

1. The restoration of native, forested riparian habitats is a widely accepted method for improving degraded streams. Little is known, however, about how the width, extent and continuity of forested vegetation along stream networks affect stream ecosystems. 2. To increase the likelihood of achieving restoration goals, restoration practitioners require quantitative tools to guide the development of restoration strategies in different catchment settings. We present an empirically based model that establishes a relationship between a ‘stress’ imposed at different locations along a stream by the spatial pattern of land cover within catchments, and the response of biologically determined ecosystem characteristics to this stress. The model provides a spatially explicit, quantitative framework for predicting the effects of changes in catchment land cover composition and spatial configuration on specific characteristics of stream ecosystems. 3. We used geospatial datasets and biological data for attached algae and benthic macroinvertebrates in streams to estimate model parameters for 40 sites in 33 distinct catchments within the mid‐Atlantic Piedmont region of the eastern U.S. Model parameters were estimated using a genetic optimisation algorithm. R² values for the resulting relationships between catchment land cover and biological characteristics of streams were substantially improved over R² values for spatially aggregated regression models based on whole‐catchment land cover. 4. Using model parameters estimated for the mid‐Atlantic Piedmont, we show how the model can be used to guide restoration planning in a case study of a small catchment. The model predicts the quantitative change in biological characteristics of the stream, such as indices of species diversity and species composition, that would occur with the implementation of a hypothetical restoration project.     

Hierarchical analysis of wild Atlantic salmon (Salmo salar) fecundity in relation to body size and developmental traits

Using data from wild Atlantic salmon Salmo salar returning to spawn in seven Scottish rivers, we developed a model of fecundity based on individual body size and key developmental traits. We used a novel approach to model selection which maximises predictive accuracy for application to target river stocks to select the best from a suite of Bayesian hierarchical models. This approach aims to ensure the optimal model within the candidate set includes covariates that best predict out-of-sample data to estimate fecundity in areas where no direct observations are available. In addition to body size, the final model included the developmental characteristics of age at smolting and years spent at sea. Using two independent long-term monitoring datasets, the consequences of ignoring these characteristics was revealed by comparing predictions from the best model with models that omitted them.