颅内压动力学仿真

颅内压(Intracranial Pressure,ICP)研究在临床上有十分重要的意义。生理上由于内外多种原因会引起颅内压变化,而同时心搏、呼吸、以及神经调节等的影响也会使颅内压出现波动。本研究在动物(犬)实验结果的基础上,建立了反映颅内压变化的集中参数数学模型。模型中包括了脑血管床、脑脊液的生成和吸收、颅脑顺应性等模块以及这些模块之间的相互作用。脑血管顺应性是表征脑血管弹性程度的重要参量,仿真采用指数拟合的脑血管容积压力实验关系来表示脑血管顺应性。模型较好地模拟了颅内压动力学以及颅内压的波动,模型参数的变化和动物实验状况的变化相吻合,可以为临床颅内压监护及诊疗提供一定的参考。     

Iterative Most-Likely Point Registration (IMLP): A Robust Algorithm for Computing Optimal Shape Alignment

We present a probabilistic registration algorithm that robustly solves the problem of rigid-body alignment between two shapes with high accuracy, by aptly modeling measurement noise in each shape, whether isotropic or anisotropic. For point-cloud shapes, the probabilistic framework additionally enables modeling locally-linear surface regions in the vicinity of each point to further improve registration accuracy. The proposed Iterative Most-Likely Point (IMLP) algorithm is formed as a variant of the popular Iterative Closest Point (ICP) algorithm, which iterates between point-correspondence and point-registration steps. IMLP’s probabilistic framework is used to incorporate a generalized noise model into both the correspondence and the registration phases of the algorithm, hence its name as a most-likely point method rather than a closest-point method. To efficiently compute the most-likely correspondences, we devise a novel search strategy based on a principal direction (PD)-tree search. We also propose a new approach to solve the generalized total-least-squares (GTLS) sub-problem of the registration phase, wherein the point correspondences are registered under a generalized noise model. Our GTLS approach has improved accuracy, efficiency, and stability compared to prior methods presented for this problem and offers a straightforward implementation using standard least squares. We evaluate the performance of IMLP relative to a large number of prior algorithms including ICP, a robust variant on ICP, Generalized ICP (GICP), and Coherent Point Drift (CPD), as well as drawing close comparison with the prior anisotropic registration methods of GTLS-ICP and A-ICP. The performance of IMLP is shown to be superior with respect to these algorithms over a wide range of noise conditions, outliers, and misalignments using both mesh and point-cloud representations of various shapes.     

A Systematic Comparison of Mathematical Models for Inherent Measurement of Ciliary Length: How a Cell Can Measure Length and Volume

Cells control organelle size with great precision and accuracy to maintain optimal physiology, but the mechanisms by which they do so are largely unknown. Cilia and flagella are simple organelles in which a single measurement, length, can represent size. Maintenance of flagellar length requires an active transport process known as intraflagellar transport, and previous measurements suggest that a length-dependent feedback regulates intraflagellar transport. But the question remains: how is a length-dependent signal produced to regulate intraflagellar transport appropriately? Several conceptual models have been suggested, but testing these models quantitatively requires that they be cast in mathematical form. Here, we derive a set of mathematical models that represent the main broad classes of hypothetical size-control mechanisms currently under consideration. We use these models to predict the relation between length and intraflagellar transport, and then compare the predicted relations for each model with experimental data. We find that three models—an initial bolus formation model, an ion current model, and a diffusion-based model—show particularly good agreement with available experimental data. The initial bolus and ion current models give mathematically equivalent predictions for length control, but fluorescence recovery after photobleaching experiments rule out the initial bolus model, suggesting that either the ion current model or a diffusion-based model is more likely correct. The general biophysical principles of the ion current and diffusion-based models presented here to measure cilia and flagellar length can be generalized to measure any membrane-bound organelle volume, such as the nucleus and endoplasmic reticulum.     

A branching process model of gene amplification following chromosome breakage.

We have devised a mathematical model of gene amplification utilizing recent experimental observations concerning dihydrofolate reductase (DHFR) gene amplification in CHO cells. The mathematical model, based on a biological model which proposes that acentric elements are the initial intermediates in gene amplification, includes the following features: (1) initiation of amplification by chromosomal breakage to produce an acentric structure; (2) replication of acentric DNA, once per cell cycle; (3) dissociation of replicated acentric DNA; (4) unequal segregation of acentric DNA fragments to daughter cells at mitosis; (5) subsequent reintegration of acentric fragments into chromosomes. These processes are assumed to be independent for each element present in a cell at a given time. Thus, processes of unequal segregation and integration may occur in parallel, not necessarily in a unique sequence, and may be reiterated in one or multiple cell cycles. These events are described mathematically as a Galton-Watson branching process with denumerable infinity of object types. This mathematical model qualitatively and quantitatively reproduces the major elements of the dynamical behavior of DHFR genes observed experimentally. The agreement between the mathematical model and the experimental data lends credence to the biological model proposed by Windle et al. (1991), including the importance of chromosome breakage and subsequent gene deletion resulting from resection of the broken chromosome ends as initial events in gene amplification.     

Understanding Streaming in <Emphasis Type="Italic">Dictyostelium discoideum</Emphasis>: Theory Versus Experiments

Recent experimental work involving Dictyostelium discoideum seems to contradict several theoretical models. Experiments suggest that localization of the release of the chemoattractant cyclic adenosine monophosphate to the uropod of the cell is important for stream formation during aggregation. Yet several mathematical models are able to reproduce streaming as the cells aggregate without taking into account localization of the chemoattractant. A careful analysis of the experiments and the theory suggests the two major features of the system which are important to stream formation are random cell motion and chemotaxis to regions of higher cell density. Random cell motion acts to reduce streaming, whereas chemotaxis to regions of higher cell density reinforces streaming. With this understanding, the experimental results can be explained in a manner consistent with the theoretical results. In all the experiments, alterations in the two main factors of random motion and chemotaxis to regions of higher cell density, not the localization of the release of the chemoattractant, can explain the results as they relate to streaming. Additionally, a comparison of results from a mathematical model that simulates cells which localize the chemoattractant and cells which do not shows little difference in the streaming patterns.     

Simulation of penicillin production in fed-batch cultivations using a morphologically structured model

A mathematical model is formulated to describe trends in biomass and penicillin formation as well as substrate consumption for fed-batch cultivations. The biomass is structured into three morphological compartments, and glucose and corn steep liquor are considered as substrates for growth. Penicillin formation is assumed to take place in the subapical compartment and in the growing region of the hyphal compartment. Furthermore, it is inhibited by glucose. Model parameters are estimated using an evolutionary algorithm and fitting the model to a standard fed-batch cultivation. The model is validated on experimental data from three different fed-batch cultivations, including two repeated fed-batch cultivations. The model predictions show good agreement with the measurements of biomass and pencillin concentrations for all fed-batch cultivations. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 56: 593-604, 1997.     

Functional order of assembly of herpes simplex virus DNA replication proteins into prereplicative site structures.

Herpes simplex virus replicates its DNA within nuclear structures called replication compartments. In contrast, in cells in which viral DNA replication is inhibited, viral replication proteins localize to punctate structures called prereplicative sites. We have utilized viruses individually mutated in each of the seven essential replication genes to assess the function of each replication protein in the assembly of these proteins into prereplicative sites. We observed that four replication proteins, UL5, UL8 UL52, and UL9, are necessary for the localization of ICP8 (UL29) to prereplicative sites natural infection conditions. Likewise, four of the seven viral DNA replication proteins, UL5, UL52, UL9, and ICP8, are necessary for the localization of the viral DNA polymerase to prereplicative sites. On the basis of these results, we present a model for prereplicative site formation in infected cells in which the helicase-primase components (UL5, UL8, and UL52), the origin-binding protein (UL9), and the viral single-stranded DNA-binding protein (ICP8) assemble together to initiate the process. This is followed by the recruitment of the viral polymerase into the structures, a step facilitated by the polymerase accessory protein, UL42. Host cell factors can apparently substitute for some of these viral proteins under certain conditions, because the viral protein requirements for prereplicative site formation are reduced in transfected cells and in infected cells treated with drugs that inhibit DNA synthesis.     

Effect of NAD recirculation on the mechanism of ATP stabilization in cytoplasm. Mathematical models]

A mathematical model of the glycolytic system with the cytoplasmic coenzymes NAD+ and NADH as essential variables is proposed. It has been shown that any increase in the steady-state concentration of NADH will reduce the range of activity of the "generalized" ATPase, wherein the level of ATP is stabilized. Such a reduction in the range of ATP stabilization may be caused by an increasing rate of the pyruvate loss into non-glycolytic pathways, in particular, into mitochondria. This effect may be compensated by increasing oxidation of NADH by the dehydrogenases of H+-transferring cytosol-mitochondrial shuttles (malate-aspartate or alpha-glycerophosphate). The properties of the complete model were compared with those of its simplified version, which takes account only of the phosphotransferase reactions of glycolysis. The effects of various factors, which do not alter the level of NADH in the system, may be studied within the scope of the simplified model.     

Modelling of growth and product formation of Porphyridium purpureum

In this contribution experimental data and simulations of growth and product formation of the unicellular microalgae Porphyridium purpureum are presented. A mathematical model has been developed for a better understanding of growth and product formation in production plants. The model has been refined with the results of several cultivations in a new photobioreactor designed especially for the study of microalgal kinetics under highly defined illumination conditions. In this photobioreactor light is generated by an external light source and then distributed by means of optical fibres into an internal draft tube which also serves as irradiation element. All cultivations were performed in turbidostate mode. The influence of different light intensity changes, including stepwise change and light-dark cycles in the range from millisecond to second, has been investigated and the results were integrated into the mathematical model. The structured mathematical model consists of three levels: metabolic flux, control of macromolecules and the reactor level. A new linear optimization approach has been realized, enabling the model to describe even very different cultivation conditions. Output variables are among others the commercially interesting macromolecules of the microalgae, e.g. polysaccharides, pigments and polyunsaturated fatty acids. Thus, reliable predictions of the specific production rates of these products are possible for the production in a larger scale.     

Epidural Intracranial Pressure Measurement in Rats Using a Fiber-optic Pressure Transducer

Elevated intracranial pressure (ICP) is a significant problem in several forms of ischemic brain injury including stroke, traumatic brain injury and cardiac arrest. This elevation may result in further neurological injury, in the form of transtentorial herniation^1,2,3,4, midbrain compression, neurological deficit or increased cerebral infarct^2,4. Current therapies are often inadequate to control elevated ICP in the clinical setting^5,6,7 . Thus there is a need for accurate methods of ICP measurement in animal models to further our understanding of the basic mechanisms and to develop new treatments for elevated ICP.In both the clinical and experimental setting ICP cannot be estimated without direct measurement. Several methods of ICP catheter insertion currently exist. Of these the intraventricular catheter has become the clinical ''gold standard'' of ICP measurement in humans⁸. This method involves the partial removal of skull and the instrumentation of the catheter through brain tissue. Consequently, intraventricular catheters have an infection rate of 6-11%⁹. For this reason, subdural and epidural cannulations have become the preferred methods in animal models of ischemic injury. Various ICP measurement techniques have been adapted for animal models, and of these, fluid-filled telemetry catheters¹⁰ and solid state catheters are the most frequently used^{11,12,13,14,15}. The fluid-filled systems are prone to developing air bubbles in the line, resulting in false ICP readings. Solid state probes avoid this problem (Figure 1). An additional problem is fitting catheters under the skull or into the ventricles without causing any brain injury that might alter the experimental outcomes. Therefore, we have developed a method that places an ICP catheter contiguous with the epidural space, but avoids the need to insert it between skull and brain. An optic fibre pressure catheter (420LP, SAMBA Sensors, Sweden) was used to measure ICP at the epidural location because the location of the pressure sensor (at the very tip of the catheter) was found to produce a high fidelity ICP signal in this model. There are other manufacturers of similar optic fibre technologies¹³ that may be used with our methodology. Alternative solid state catheters, which have the pressure sensor located at the side of the catheter tip, would not be appropriate for this model as the signal would be dampened by the presence of the monitoring screw. Here, we present a relatively simple and accurate method to measure ICP. This method can be used across a wide range of ICP related animal models.     

Connecting biology and mechanics in fracture healing: an integrated mathematical modeling framework for the study of nonunions

Both mechanical and biological factors play an important role in normal as well as impaired fracture healing. This study aims to provide a mathematical framework in which both regulatory mechanisms are included. Mechanics and biology are coupled by making certain parameters of a previously established bioregulatory model dependent on local mechanical stimuli. To illustrate the potential added value of such a framework, this coupled model was applied to investigate whether local mechanical stimuli influencing only the angiogenic process can explain normal healing as well as overload-induced nonunion development. Simulation results showed that mechanics acting directly on angiogenesis alone was not able to predict the formation of overload-induced nonunions. However, the direct action of mechanics on both angiogenesis and osteogenesis was able to predict overload-induced nonunion formation, confirming the hypotheses of several experimental studies investigating the interconnection between angiogenesis and osteogenesis. This study shows that mathematical models can assist in testing hypothesis on the nature of the interaction between biology and mechanics.     

A discrete cell model with adaptive signalling for aggregation of Dictyostelium discoideum.

Dictyostelium discoideum (Dd) is a widely studied model system from which fundamental insights into cell movement, chemotaxis, aggregation and pattern formation can be gained. In this system aggregation results from the chemotactic response by dispersed amoebae to a travelling wave of the chemoattractant cAMP. We have developed a model in which the cells are treated as discrete points in a continuum field of the chemoattractant, and transduction of the extracellular cAMP signal into the intracellular signal is based on the G protein model developed by Tang & Othmer. The model reproduces a number of experimental observations and gives further insight into the aggregation process. We investigate different rules for cell movement the factors that influence stream formation the effect on aggregation of noise in the choice of the direction of movement and when spiral waves of chemoattractant and cell density are likely to occur. Our results give new insight into the origin of spiral waves and suggest that streaming is due to a finite amplitude instability.     

Measurement,control, and modeling of submerged acetic acid fermentation

For control and optimization of large scale bioprocesses, mathematical models are needed to describe transient growth and/or product formation. Such models can only be developed from reliable experimental data. A computerized experimental system was applied to submerged acetic acid fermentation with industrial Acetobacter strains in order to obtain quantitatively reproducible long-term data. Automated repeated-batch fermentations were carried out over a period of one year. It was found that consideration of substrate, product, and biomass concentrations alone was not sufficient to describe transient culture conditions. At least one more internal parameter must be taken into account. A delay-time model was developed which takes into consideration the variable concentration of an internal component of the cells, the ribonucleic acid. This model was used to simulate the acetic acid fermentation. The simulation results agreed well with the experimental data. Thus, the validity of the model assumptions could be confirmed. The model was capable of simulating the lag-phase of growth as well as lysis of microorganisms due to product inhibition.     

A mathematical framework for inferring connectivity in probabilistic neuronal networks

We describe an approach for determining causal connections among nodes of a probabilistic network even when many nodes remain unobservable. The unobservable nodes introduce ambiguity into the estimate of the causal structure. However, in some experimental contexts, such as those commonly used in neuroscience, this ambiguity is present even without unobservable nodes. The analysis is presented in terms of a point process model of a neuronal network, though the approach can be generalized to other contexts. The analysis depends on the existence of a model that captures the relationship between nodal activity and a set of measurable external variables. The mathematical framework is sufficiently general to allow a large class of such models. The results are modestly robust to deviations from model assumptions, though additional validation methods are needed to assess the success of the results.     

Phenotype of the herpes simplex virus type 1 protease substrate ICP35 mutant virus.

The herpes simplex virus type 1 ICP35 assembly protein is involved in the formation of viral capsids. ICP35 is encoded by the UL26.5 gene and is specifically processed by the herpes simplex virus type 1 protease encoded by the UL26 gene. To better understand the functions of ICP35 in infected cells, we have isolated and characterized an ICP35 mutant virus, delta ICP35. The mutant virus was propagated in complementing 35J cells, which express wild-type ICP35. Phenotypic analysis of delta ICP35 shows that (i) mutant virus growth in Vero cells was severely restricted, although small amounts of progeny virus was produced; (ii) full-length ICP35 protein was not produced, although autoproteolysis of the protease still occurred in mutant-infected nonpermissive cells; (iii) viral DNA replication of the mutant proceeded at wild-type levels, but only a very small portion of the replicated DNA was processed to unit length and encapsidated; (iv) capsid structures were observed in delta ICP35-infected Vero cells by electron microscopy and by sucrose sedimentation analysis; (v) assembly of VP5 into hexons of the capsids was conformationally altered; and (vi) ICP35 has a novel function which is involved in the nuclear transport of VP5.     

Dialysis Continuous Process for Ammonium-Lactate Fermentation: Improved Mathematical Model and Use of Deproteinized Whey

Separate terms for substrate limitation and product inhibition were incorporated into an equation describing the rate of cell growth for the steady-state fermentation of lactose to lactic acid with neutralization to a constant pH by ammonia. The equation was incorporated into a generalized mathematical model of a dialysis continuous process for the fermentation, developed previously, in which the substrate is fed into the fermentor and the fermentor contents are dialyzed through a membrane against water. The improved model was used to simulate the fermentation on a digital computer, and the results agreed with previous experimental tests using whole whey as the substrate. Further simulations were then made to guide experimental tests using deproteinized whey as the substrate. Dried cheese-whey ultrafiltrate was rehydrated with tap water to contain 242 mg of lactose per ml, supplemented with 8 mg of yeast extract per ml, charged into a 5-liter fermentor without sterilization, adjusted in pH (5.5) and temperature (44°C), and inoculated with an adapted culture of Lactobacillus bulgaricus. The fermentor and dialysate circuits were connected, and a series of steady-state conditions was managed nonaseptically for 71 days. The fermentation of deproteinized whey relative to whole whey, with both highly concentrated, resulted in similar extents of product accumulation but at a lesser rate.     

The Bipolar Filaments Formed by Herpes Simplex Virus Type 1 SSB/Recombination Protein (ICP8) Suggest a Mechanism for DNA Annealing

Herpes simplex virus type 1 encodes a multifunctional protein, ICP8, which serves both as a single-strand binding protein and as a recombinase, catalyzing reactions involved in replication and recombination of the viral genome. In the presence of divalent ions and at low temperature, previous electron microscopic studies showed that ICP8 will form long left-handed helical filaments. Here, electron microscopic image reconstruction reveals that the filaments are bipolar, with an asymmetric unit containing two subunits of ICP8 that constitute a symmetrical dimer. This organization of the filament has been confirmed using scanning transmission electron microscopy. The pitch of the filaments is ∼ 250 Å, with ∼ 6.2 dimers per turn. Docking of a crystal structure of ICP8 into the reconstructed filament shows that the C-terminal domain of ICP8, attached to the body of the subunit by a flexible linker containing ∼ 10 residues, is packed into a pocket in the body of a neighboring subunit in the crystal in a similar manner as in the filament. However, the interactions between the large N-terminal domains are quite different in the filament from that observed in the crystal. A previously proposed model for ICP8 binding single-stranded DNA (ssDNA), based upon the crystal structure, leads to a model for a continuous strand of ssDNA near the filament axis. The bipolar nature of the ICP8 filaments means that a second strand of ssDNA would be running through this filament in the opposite orientation, and this provides a potential mechanism for how ICP8 anneals complementary ssDNA into double-stranded DNA, where each strand runs in opposite directions.