Lake sediment records of erosional processes

Accumulations of sediment at the beds of lakes, estuaries and reservoirs provide partial records of materials transported from the surrounding water catchment areas. Physical, chemical, biological and magnetic analyses, with data for accumulation rates, have been used in a range of environmental settings to infer the rate, form, cause and source of erosion. This paper is a brief review of these studies from a hydrological perspective, setting sediment studies within a lake-catchment system. The need for long term erosional records is discussed in terms of the type of erosional data which may be obtained. Alternative approaches to studying short and long term erosion are assessed with regard to their cost-effectiveness and their levels of precision and accuracy. Finally, some suggestions are made about how these erosion records may be used to model hydrological, pedological and geomorphological processes, thus linking together long term, short term and contemporary timescales of process operation.     

Microtubule Patterning in the Presence of Stationary Motor Distributions

In this paper, we construct a novel nonlocal transport model that describes the evolution of microtubules (MTs) as they interact with stationary distributions of motor proteins. An advection term accounts for directed MT transport (sliding due to motor protein action), and an integral term accounts for reorientation of MTs due to their interactions with cross-linking motor proteins. Simulations of our model show how MT patterns depend on boundary constraints, as well as model parameters that represent motor speed, cross-linking capability (motor activity), and directionality. In large domains, and using motor parameter values consistent with experimentally-derived values, we find that patterns such as asters, vortices, and bundles are able to persist. In vivo, MTs take on aster patterns during interphase and they form bundles in neurons and polarized epithelial cells. Vortex patterns have not been observed in vivo, however, are found in in vitro experiments. In constrained domains, we find that similar patterns form (asters, bundles, and vortices). However, we also find that when two opposing motors are present, anti-parallel bundles are able to form, resembling the mitotic spindle during cell division. This model demonstrates how MT sliding and MT reorientation are sufficient to produce experimentally observed patterns.     

一个具有时滞的媒介传播流行病模型中的Hopt分支（英文）

文章研究的是一个具有时滞的媒介传播流行病模型.假定长期的发病率是双线性大规模行动的方式,确定了疾病是否流行的阈值R_0.当R_0≤1时,得到无病平衡点是全局稳定的,即疾病消失;当R_0〉1时,得到地方病平衡点.在具有时滞的微分模型中,时滞与载体转变成传染源的孵化期有关。我们研究了时滞对平衡点稳定性的影响,研究表明,在从寄生源到载体的传播过程中,时滞可以破坏动力系统并且得到了Hopt分支的周期解.     

The role of higher predation in plankton population models

Zooplankton mortality in plankton population models is oftenrepresented by the so-called closure term. Recently, much attentionhas been paid to the choice of functional form used for theclosure term, primarily due to the influential paper by Steeleand Henderson (J. Plankton Res., 14, 157–172, 1992). Herewe reveal an inconsistency in the normalization of Steele andHenderson's models, and show that unforced short-term oscillations(limit cycles) can occur when a quadratic closure term is used.Furthermore, we contradict the hypothesis regarding the relationshipbetween nutrient steady-state values and the choice of closureterm: using the seven-component plankton model of Fasham (TheGlobal Carbon Cycle, Heimann,M. (ed.), pp. 457–504, 1993)with four alternative closure terms, we find the nutrient valueto depend more upon the choice of parameter values than on thechoice of closure term. However, our results agree with andstrengthen the general conclusion of Steele and Henderson'swork: that the choice of closure term can strongly influencethe dynamics of models.     

Short term synaptic depression imposes a frequency dependent filter on synaptic information transfer

Depletion of synaptic neurotransmitter vesicles induces a form of short term depression in synapses throughout the nervous system. This plasticity affects how synapses filter presynaptic spike trains. The filtering properties of short term depression are often studied using a deterministic synapse model that predicts the mean synaptic response to a presynaptic spike train, but ignores variability introduced by the probabilistic nature of vesicle release and stochasticity in synaptic recovery time. We show that this additional variability has important consequences for the synaptic filtering of presynaptic information. In particular, a synapse model with stochastic vesicle dynamics suppresses information encoded at lower frequencies more than information encoded at higher frequencies, while a model that ignores this stochasticity transfers information encoded at any frequency equally well. This distinction between the two models persists even when large numbers of synaptic contacts are considered. Our study provides strong evidence that the stochastic nature neurotransmitter vesicle dynamics must be considered when analyzing the information flow across a synapse.     

Zinc metabolism in humans: a kinetic model

The development and testing of an integrated kinetic model describing both short and long term zinc metabolism in humans is discussed. The development took place in two stages. The first, based on a five day turnover study, details the early phases of zinc metabolism in several body tissues together with absorption and excretion. This model, however, accounts for only 10% of total body zinc. To describe the kinetics of total body zinc, a long term model which contains a reduced version of the five day model was developed. This model required an additional compartment for the liver system, but as postulated in the short term model, 90% of body zinc turns over slowly in a single compartment. The models are then used to describe the effect on zinc metabolism of different disease states and lietary perturbations. These additional studies enhance the models' validity while providing physiological insights.     

An unstructured model for studies on phenanthrene bioconversion by filamentous fungus Cunninghamella elegans

An unstructured model for phenanthrene bioconversion by filamentous fungus Cunnighamella elegans in stirred tank batch bioreactors was proposed. It was observed that the process of phenanthrene bioconversion is strictly associated with exponential growth of biomass. Therefore, a Monod-type, with Contois term, unstructured model could be applied to describe the process mathematically. The inhibition of biomass growth due to high concentrations of phenanthrene present in the medium was taken into account in the form of Yerusalimski's uncompetitive inhibition term.     

Exponential growth in age-structured two-sex populations

We consider a continuous age-structured two-sex population model which is given by a semilinear system of partial differential equations with nonlocal boundary conditions and is a simpler case of Fredrickson-Hoppensteadt model. The non-linearity is introduced by a source term, called from its physical meaning, the marriage function. The explicit form of the marriage function is not known; however, there is an understanding among the demographers about the properties it should satisfy. We have shown that the homogeneity property of the non-linearity leads to the fact that the system supports exponentially growing persistent solutions using a general form of the marriage function and its properties. This suggests that the model can be viewed as a possible extension of the one-sex stable population theory to monogamously mating two-sex populations.     

海马记忆功能的神经网络模型

综合神经心理学,神经生理学、解剖学与神经网络研究的成果,提出一个海马记忆功能的神经网络模型。模型由三个神经网络所组成;海马的ＣＡ１和ＣＡ３网络和大脑皮层联合区,ＣＡ３的功能是将不同感觉输入联合起来,而ＣＡ１的作用是将它们结成一个单一的记忆。而大脑皮层则是长期记忆的部位。在ＶＡＸ１１／７５０上进行计算机仿真,仿真证明模型有近期及长期记忆功能,破坏模拟海马的部分,模型显示出与顺行性遗忘症相似的特性。在     

SPATIOTEMPORAL VARIATION OF THE ABUNDANCE OF CALCAREOUS GREEN MACROALGAE IN THE FLORIDA KEYS: A STUDY OF SYNCHRONY WITHIN A MACROALGAL FUNCTIONAL‐FORM GROUP1

The abundance of calcareous green algae was recorded quarterly at 28 sites within the Florida Keys National Marine Sanctuary (FKNMS) for a period of 7 years as part of a sea grass monitoring program. To evaluate the validity of using the functional‐form group approach, we designed a sampling method that included the functional‐form group and the component genera. This strategy enabled us to analyze the spatiotemporal patterns in the abundance of calcareous green algae as a group and to describe synchronous behavior among its genera through the application of a nonlinear regression model to both categories of data. Spatial analyses revealed that, in general, all genera displayed long‐term trends of increasing abundance at most sites; however, at some sites the long‐term trends for genera opposed one another. Strong synchrony in the timing of seasonal changes was found among all genera, possibly reflecting similar reproductive and seasonal growth pattern, but the variability in the magnitude of seasonal changes was very high among genera and sites. No spatial patterns were found in long‐term or seasonal changes; the only significant relation detected was for slope, with sites closer to land showing higher values, suggesting that some factors associated with land proximity are affecting this increase. We conclude that the abundances of genera behaved differently from the functional‐form group, indicating that the use of the functional‐form group approach may be unsuitable to detect changes in sea grass community structure in the FKNMS at the existing temporal and spatial scale of the monitoring program.     

Calculation of the g-factors of hemoproteins with the crystal field theory. Development of a 3-term model

A 3-term crystal field model is used for the calculation of the magnetic properties of ferric hemoproteins. This model includes the high spin term (6A1), the low spin term (2T2) and the quartet term (4T1). The pertubation matrix between these 3 terms caused by spin orbit coupling and ligand fields of cubic, axial and rhombic symmetry are evaluated. The g-factor of the low spin cytochrome P-450 LM2 from rabbit liver are calculated using this 3-term model and the results are compared with those from the usual 1-term model. Contrary to the 1-term model, no orbital moment correction factor is necessary. That means that the orbital moment correction factor with value > 1 simulates some term interaction, predominantly with the quartet term. The g-factors of the high spin cytochrome P-450 LM4 were also calculated by means of the 3-term model and compared with a spin hamilton treatment. A good agreement between the spin hamilton parameters derived from the experimental g-factors and those calculated by the 3-term model were obtained. For hemoproteins with strongly mixed spin states the 3-term model is also useful, contrary to 1-term models or spin hamiltonians which are completely incorrect. The 3-term model is a minimal model to describe all typical magnetic properties of low spin and high spin ferric hemoproteins with the smallest number of terms.     

Effects of changes in the driving forces on water quality and plankton dynamics in three Swiss lakes – long‐term simulations with BELAMO

1. With a modified version of the lake model BELAMO, we were able to describe the essential features of the dynamics of nutrients, dissolved oxygen, phyto‐ and zooplankton in three lakes of different trophic status over periods of 19–30 years, with essentially the same model parameters for all three lakes. This is remarkable, as the measured nutrient inputs decreased considerably during the simulated time period. 2. Despite having done this before for a period of 4 years with an earlier version of the model, a considerable effort was required that led to a series of model modifications without which the data could not be matched. This demonstrates that long‐term calibration of a model that combines processes in the water column with mineralisation in the sediment can be difficult. 3. Due to the necessarily simplified processes within the model, there is a bias in its output. We applied a recently developed technique for model calibration and uncertainty analysis to address bias and multiple calibration criteria. To account for the demanding long‐term simulations, a simplified numerical implementation of this technique was used. 4. Our results demonstrate good understanding of the chemical state of the lake during the calibration period but less of the biological variables. The credibility intervals used to visualise this knowledge widen substantially during the prediction period (consisting of the last 10 years of the simulation). 5. The joint calibration of the model with long‐term data from lakes of different trophic status is possible but only with considerable prediction uncertainty. Due to the explicit consideration of bias in our calibration technique, we are able to estimate quantitatively the uncertainty of our knowledge about chemical and biological variables in the lake.     

Marcus treatment of endergonic reactions: a commentary

Two forms of the equation for expression of the rate constant for electron transfer through a Marcus-type treatment are discussed. In the first (exergonic) form, the Arrhenius exponential term was replaced by its classical Marcus term; in the second (endergonic) form, the forward rate constant was replaced by the reverse rate constant (the forward rate constant in the exergonic direction), which was expanded to an equivalent Marcus term and multiplied by the equilibrium constant. When the classical Marcus treatment was used, these two forms of the rate equation give identical curves relating the logarithm of the rate constant to the driving force. The Marcus term for the relation between activation free-energy, DeltaG#, reorganization energy, lambda, and driving force, DeltaG(o), derived from parabolas for the reactant and product states, was identical when starting from exergonic or endergonic parabolas. Moser and colleagues introduced a quantum mechanical correction factor to the Marcus term in order to fit experimental data. When the same correction factor was applied in the treatment for the endergonic direction by Page and colleagues, a different curve was obtained from that found with the exergonic form. We show that the difference resulted from an algebraic error in development of the endergonic equation.     

Estimation and prediction of cell cycle specific effects of anticancer drugs

A mathematical model is used to estimate the cell cycle phase specific action of a new anticancer drug, CI-921, based on results of a short term (8 hr) stathmokinetic (blocked divisions) study on Friend leukemia cells. The estimate obtained is in the form of a sequence of fractions of the cell flow blocked in successive subcompartments of the cell cycle. At specific drug concentrations, the information contained in this estimate is sufficient to correctly predict the results of long term (24 hr) continuous drug exposure. The result obtained seems to be of interest, since the ability to predict the cell cycle phase specific effects of anticancer drugs is crucial for any attempt to improve the existing chemotherapeutic treatment schedules for cancer. This study required developing new mathematical techniques, among them a nonparametric method for estimation of the distributions of cell residence times in the G₁ phase of the cell cycle (Appendix). The methods developed are general enough to be applicable, in principle, to any chemotherapeutic agent the action of which is distributed throughout the cell cycle.     

Lymphangiogenesis in vitro: Formation of lymphatic capillary-like channels from confluent monolayers of lymphatic endothelial cells

Summary Lymphatic endothelial cells grown long term in culture form lymphatic capillarylike tubes. Examination by light and transmission electron microscopy showed that these structures were closed loops composed of one to several cells connected by intercellular junction to form a luminal space. This first demonstration of lymphangiogenesis in confluent monolayer cultures of lymphatic endothelial cells (a) showed that collagen type I accelerated lymphatic capillary tube formation, whereas fibronectin and matrigel had no effect; b) provided a model to study lymphatic endothelial cell function and differentiation; and c) offered a possibility to distinguish differences between the process of lymphangiogenesis and angiogenesis by testing various factors and conditions that effect endothelial cell behavior.     

A new distance for high level RNA secondary structure comparison

We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling classically used in the literature. This allows us to address some serious limitations of the more traditional tree edit operations when the trees represent RNAs and what is searched for is a common structural core of two RNAs. Although the algorithm complexity has an exponential term, this term depends only on the number of successive fusions that may be applied to a same node, not on the total number of fusions. The algorithm remains therefore efficient in practice and is used for illustrative purposes on ribosomal as well as on other types of RNAs.     

Organotypic heart slices for cell transplantation and physiological studies

Recent studies have significantly improved our ability to investigate cell transplantation and study the physiology of transplanted cells in cardiac tissue. Several previous studies have shown that fully-immersed heart slices can be used for electrophysiological investigations. Additionally, ischemic heart slices induced by glucose and oxygen deprivation offer a useful tool to investigate mechanical integration and to measure forces of contraction of engrafted cells, at least for short term analysis. A recent and novel model of heart slices, prepared from rat and human tissues, can be maintained in culture for up to two months. This new heart slice model can be used for long term in vitro cell transplantation studies and for pharmacological evaluation. This review will focus on describing these models and demonstrating the use of organotypic heart slices as a novel tool for drug, for studying electrophysiology and for developing cellular therapeutic approaches to alleviate cardiac tissue damage.     

Theorizing transnational immigration: a critical review of current efforts

During the past decade, transnationalism has entered the lexicon of migration scholars. As with other terms used in the study of immigration and ethnicity, this concept suffers from ambiguity as a result of competing definitions that fail to specify the temporal and spatial parameters of the term and to adequately locate it vis-à-vis older concepts such as assimilation and cultural pluralism. This article offers a review and critique of the ways the term has come to be employed at the hands of key spokespersons that have articulated the most sustained theoretical rationales to date for transnationalism as a conceptual construct to account for new immigrant identities and communities. The conclusion of the essay offers in schematic form an alternative assessment of transnationalism that locates it as one potential subset of assimilation theory, rather than as an alternative to it.