Feller processes: the next generation in modeling. Brownian motion, Lévy processes and beyond

We present a simple construction method for Feller processes and a framework for the generation of sample paths of Feller processes. The construction is based on state space dependent mixing of Lévy processes. Brownian Motion is one of the most frequently used continuous time Markov processes in applications. In recent years also Lévy processes, of which Brownian Motion is a special case, have become increasingly popular. Lévy processes are spatially homogeneous, but empirical data often suggest the use of spatially inhomogeneous processes. Thus it seems necessary to go to the next level of generalization: Feller processes. These include Lévy processes and in particular brownian motion as special cases but allow spatial inhomogeneities. Many properties of Feller processes are known, but proving the very existence is, in general, very technical. Moreover, an applicable framework for the generation of sample paths of a Feller process was missing. We explain, with practitioners in mind, how to overcome both of these obstacles. In particular our simulation technique allows to apply Monte Carlo methods to Feller processes.     

What are the policy priorities for sustaining ecological processes? A case study from Victoria,Australia

Summary Developments in ecological theory indicate that ecological processes have major implications for sustaining biodiversity and the provision of ecosystem services. Consequently, conservation actions that focus solely on particular species, vegetation communities, habitats or sites (‘assets’) are unlikely to be effective over the long term unless the ecological processes that support them continue to function. Efforts to sustain biodiversity must embrace both ‘assets’ and ‘process‐oriented’ approaches. Existing knowledge about ecological processes, incomplete though it is, has not been adequately considered in government decision making. It is, therefore, necessary to consider how to build consideration of ecological processes into legislative and institutional frameworks, policy and planning processes, and on‐ground environmental management. Drawing on insights from interviews, a facilitated workshop, and a literature review, this paper identifies a suite of policy priorities and associated reforms which should assist in ensuring that ecological processes are given more attention in policy‐making processes. It is concluded that a multi‐pronged approach is required, because there are no ‘silver bullets’ for sustaining ecological processes.     

Learning and selection

Are learning processes selection processes? This paper takes a slightly modified version of the account of selection presented in Hull et al. (Behav Brain Sci 24:511–527, 2001) and asks whether it applies to learning processes. The answer is that although some learning processes are selectional, many are not. This has consequences for teleological theories of mental content. According to these theories, mental states have content in virtue of having proper functions, and they have proper functions in virtue of being the products of selection processes. For some mental states, it is plausible that the relevant selection process is natural selection, but there are many for which it is not plausible. One response to this (due to David Papineau) is to suggest that the learning processes by which we acquire non-innate mental states are selection processes and can therefore confer proper functions on mental states. This paper considers two ways in which this response could be elaborated, and argues that neither of them succeed: the teleosemanticist cannot rely on the claim that learning processes are selection processes in order to justify the attribution of proper functions to beliefs.     

生态水文过程研究进展

生态水文学是研究生态格局和生态过程变化水文学机制的科学。它的一个重要研究方向是在不同时空尺度上和一系列环境条件下探讨生态水文过程。生态水文过程是指水文过程与生物动力过程之间的功能关系 ,它包括生态水文物理过程、生态水文化学过程及其生态效应。在探讨以上基本概念和总结生态水文过程研究特点的基础上 ,着重探讨生态水文物理过程、生态水文化学过程及其生态效应等生态水文过程核心内容的研究进展 ,并简要分析了生态水文过程研究中存在的主要问题和未来的研究热点。     

Spatial heterogeneity and function of voltage- and ligand-gated ion channels in retinal amacrine neurons.

The spatial distribution of ion channels within amacrine cells of the tiger salamander retina was studied using patch recording in the retinal slice preparation. By focally puffing kainate, GABA and glycine at amacrine cell processes in the inner plexiform layer, it was determined that the cell's glutamate receptors were located in a confined region of the processes near the soma, while glycine and GABA receptors were located throughout the processes. Likewise, similar techniques in conjunction with voltage steps demonstrated that voltage-gated sodium channels were located throughout the cell and were shown to generate sodium-dependent spikes, while only the processes contained voltage-gated calcium channels. These results suggest that this form of transient amacrine cell collects its excitatory synaptic inputs in a region confined to a central annular region near the soma, that the signal is actively propagated throughout its processes by voltage-gated sodium channels and that calcium-dependent neurotransmitter release of glycine from this neuron can occur throughout its processes. Thus, excitatory signals are collected in the processes near the soma, inhibitory signals throughout the processes and excitation is probably propagated throughout the processes of the amacrine cell.     

Enthalpy–entropy compensation phenomena in water solutions of proteins and small molecules: A ubiquitous properly of water

This article presents evidence for the existence of a specific linear relationship between the entropy change and the enthalpy change in a variety of processes of small solutes in water solution. The processes include solvation of ions and nonelectrolytes, hydrolysis, oxidation–reduction, ionization of weak electrolytes, and quenching of indole fluorescence among others. The values of the proportionality constant, called the compensation temperature, lie in a relatively narrow range, from about 250 to 315 °K, for all these processes. Such behavior can be a consequence of experimental errors but for a number of the processes the precision of the data is sufficient to show that the enthalpy–entropy compensation pattern is real. It is tentatively concluded that the pattern is real, very common and a consequence of the properties of liquid water as a solvent regardless of the solutes and the solute processes studied. As such the phenomenon requires that theoretical treatments of solute processes in water be expanded by inclusion of a specific treatment of the characteristic of water responsible for compensation behavior. The possible bases of the effect are proposed to be temperature-independent heat-capacity changes and/or shifts in concentrations of the two phenomenologically significant species of water. The relationship of these alternatives to the two-state process of water suggested by spectroscopic and relaxation studies is examined. The existence of a similar and probably identical relationship between enthalpy and entropy change in a variety of protein reactions suggests that liquid water plays a direct role in many protein processes and may be a common participant in the physiological function of proteins. It is proposed that the linear enthalpy–entropy relationship be used as a diagnostic test for the participation of water in protein processes. On this basis the catalytic processes of chymotrypsin and acetylcholinesterase are dominated by the properties of bulk water. The binding of oxygen by hemoglobin may fall in the same category. Similarities and differences in the behavior of small-solute and protein processes are examined to show how they may be related. No positive conclusions are established, but it is possible that protein processes are coupled to water via expansions and contractions of the protein and that in general the special pattern of enthalpy–entropy compensation is a consequent of the properties of water which require that expansions and contractions of solutes effect changes in the free volume of the nearby liquid water. It is shown that proteins can be expected to respond to changes in nearby water and interfacial free energy by expansions and contractions. Such responses may explain a variety of currently unexplained characteristics of protein solutions. More generally, the enthalpy–entropy compensation pattern appears to be the thermodynamic manifestation of “structure making” and “structure breaking,” operationally defined terms much used in discussions of water solutions. If so, the compensation pattern is ubiquitous and requires re-examination of a large body of molecular interpretations derived from quantitative studies of processes in water. Theories of processes in water may have to be expanded to accommodate this aspect of water behavior.     

Some myths and messages concerning the batch and continuous culture of animal cells

lt is often assumed that continuous processes are more difficult and less productive than a suite of batch processes for the production of a particular biomolecule. This paper cites two papers which have appeared in the literature which propound this view and examines in detaü the justification for the support of this contention. After reviewing those features where it is alleged that continuous processes are at a disadvantage, the authors of this paper conclude that the opposite is the case and that for suitable processes the most effective way of generating product is by the use of fully continuous processes. The choice of a particular process dependends on a variety of fixed and variable factors which are unique to the process. These factors are discussed and two decision trees are presented which are designed to facilitate the choice of the appropriate process technology. This revised version was published online in July 2006 with corrections to the Cover Date.     

SUBSTITUTION PROCESSES IN MOLECULAR EVOLUTION. II. EXCHANGEABLE MODELS FROM POPULATION GENETICS

Substitution processes are of two sorts: origination processes record the times at which nucleotide mutations that ultimately fix in the population first appear, and fixation processes record the times at which they actually fix. Substitution processes may be generated by combining models of population genetics—here the symmetrical-neutral, overdominance, underdominance, TIM, and SAS-CFF models—with the infinite-sites, no-recombination model of the gene. This paper is mainly concerned with a computer simulation study of these substitution processes. The rate of substitution is shown to be remarkably insensitive to the strength of selection for models with strong balancing selection caused by the genealogical drift of mutations through alleles held in the population by selection. The origination process is shown to be more regular than Poisson for the overdominance, TIM, and SAS-CFF models but more clustered for the underdominance model. A class of point processes called Sawyer processes is introduced to help explain these observations as well as the observation that the times between successive originations are nearly uncorrelated. Fixation processes are shown to be more complex than origination processes, with regularly spaced bursts of multiple fixations. An approximation to the fixation process is described. One important conclusion is that protein evolution is not easily reconciled with any of these models without adding perturbations that recur on a time scale that is commensurate with that of molecular evolution.     

Interrelated mechanisms in reward and learning

This brief review is focused on recent work in our laboratory, in which we assayed nicotine-induced neurotransmitter changes, comparing it to changes induced by other compounds and examined the receptor systems and their interactions that mediate the changes. The primary aim of our studies is to examine the role of neurotransmitter changes in reward and learning processes. We find that these processes are interlinked and interact in that reward-addiction mechanisms include processes of learning and learning-memory mechanisms include processes of reward. In spite being interlinked, the two processes have different functions and distinct properties and our long-term aim is to identify factors that control these processes and the differences among the processes. Here, we discuss reward processes, which we define as changes examined after administration of nicotine, cocaine or food, each of which induces changes in neurotransmitter levels and functions in cognitive areas as well as in reward areas. The changes are regionally heterogeneous and are drug or stimulus specific. They include changes in the transmitters assayed (catecholamines, amino acids, and acetylcholine) and also in their metabolites, hence, in addition to release, uptake and metabolism are involved. Many receptors modulate the response with direct and indirect effects. The involvement of many transmitters, receptors and their interactions and the stimulus specificity of the response indicated that each function, reward and learning represents the involvement of different pattern of changes with a different stimulus, therefore, many different learning and many different reward processes are active, which allow stimulus specific responses. The complex pattern of reward-induced changes in neurotransmitters is only a part of the multiple changes observed, but one which has a crucial and controlling function.     

Comparison of microbial communities in four different composting processes as evaluated by denaturing gradient gel electrophoresis analysis

AIMS: We aimed to systematically understand the composting processes by a comparison of microbial communities during four full-scale composting processes. METHODS AND RESULTS: Microbial communities during the four different full-scale composting processes were analysed by denaturing gradient gel electrophoresis combined with measurement of physicochemical parameters. Two composting processes utilized sewage sludge and two utilized food-waste. Comparison of the four processes indicated that the concentration of dissolved organic carbon was higher in the food-waste-composting than in the sewage-sludge-composting processes, and microbial communities varied with composting substrate. The tendency for different microbes to appear in the composting process with different concentrations of dissolved organic carbon agreed with a previous study that showed that microbial succession occurred with a decrease in dissolved organic carbon in a laboratory-scale food-waste-composting process. CONCLUSIONS: Our results suggested that the main factor affecting microbial communities in the composting process is the concentration of dissolved organic materials. SIGNIFICANCE AND IMPACT OF THE STUDY: In addition to studying microbial communities involved in composting, this research is also the first to study composting mechanisms using molecular methods. The results of our studies may be helpful in the design and management of composting processes.     

Relative influence of deterministic processes on structuring marsh plant communities varies across an abiotic gradient

Understanding the processes determining community structure is one of the major goals of ecological research. Both deterministic and stochastic processes may shape community structure. The challenge is to understand the relative influence of each type of process across different environmental conditions. We investigated the influence of deterministic and stochastic processes on plant community assembly in tidal marshes across a strong abiotic (salinity) gradient in three estuaries in Georgia, USA using probabilistic Raup–Crick community dissimilarity. Our results indicated that deterministic processes had an increasingly important influence on structuring plant communities in salt and brackish marshes, probably due to high heterogeneity of microhabitats produced by the interplay between abiotic stress and biotic interactions. In contrast, the influence of deterministic processes on plant community assembly decreased in tidal freshwater marshes, suggesting an increasingly important role of stochastic processes in plant community assembly in tidal freshwater marshes, probably due to the higher species richness, higher recruitment from seed, and lower levels of abiotic stress in these habitats. At the estuarine scale (across tidal freshwater, brackish and salt marshes in each estuary), our results suggested that deterministic processes also had a relatively important influence on shaping plant community structure. Our results illustrated that plant community structure in tidal marshes is influenced by both deterministic and stochastic processes, but that the relative influence of these two types of processes varies across estuarine landscapes.     

Fine structure of the epidermis of the optic tentacle in a slug, Limax flavus L.

The epidermis at the tip of the optic tentacle in Limax flavus is constructed of columnar epithelial cells, distal processes of nerve cells, and scattered processes of the collar cells. The epithelial cells extend stout microvilli called plasmatic processes by Wright perpendicularly from the free surface. Each plasmic process branches into a few terminal twigs embedded in a fuzzy filamentous substance. Most nerve cells have their nuclei under the basal lamina. The distal processes of these nerve cells reach the free surface and send long microvilli to form the spongy layer under a filamentous covering. At the side surface of the tentacle the epithelial cells are cuboidal or squamous and the neural elements are fewer. Here, no spongy layer is formed; and the collar cell processes are replaced by the lateral cell processes. Peculiar secretion granules are contained in the lateral and collar cell processes as well as in their cell bodies situated beneath the basal lamina.     

湿地氮素传输过程研究进展

综述了湿地氮素传输过程的研究进展。湿地氮素传输过程包括物理过程、化学过程和生物过程 ,与土壤、植物的发生、发育紧密联系在一起 ,并形成了空气 -水 -土 -生命系统中物质循环和能量流动的复杂网络。湿地硝态氮的淋失直接威胁着湿地地下水水质安全 ,N2 O源汇转变受土壤和水体等环境因子的制约 ,氨挥发则与水体 p H值密切相关排放。湿地氮素的化学转化过程是矿质养分供给和 N2 O产生的主要机制 ,受环境因子和人类活动干扰的影响 ;动力学模型可用于描述氮素的化学转化过程。湿地植物的吸收和累积以及微生物的分解过程是湿地氮素循环的重要环节。最后分析了当前国内外研究中存在的不足 ,并对未来研究的重点领域进行了展望     

Juvenile and mature MAP2 isoforms induce distinct patterns of process outgrowth.

Microtubule-associated protein-2 (MAP2) is the most abundant MAP in neurons, where its distribution is restricted to the somatodendritic compartment. This molecule undergoes developmentally regulated alternative splicing, resulting in at least two isoforms, a juvenile isoform (termed MAP2c) and a mature isoform (MAP2), with greatly different molecular masses. Spodoptera frugiperda (Sf9) cell expression of the juvenile versus the mature MAP2 isoform generates two distinct patterns of process outgrowth. The smaller juvenile isoform induces multiple short thin processes. Mature MAP2 tends to induce single processes that are considerably thicker than those processes induced by juvenile MAP2. We found important differences in the variability of spacing between microtubules and the number of microtubules along the processes induced by MAP2c and mature MAP2. MAP2c showed variability with most microtubules spaced as closely as with tau, but some spaced as far apart as with mature MAP2. Over their length, the mature MAP2 processes demonstrate proximo-distal taper, which corresponds to a narrowing of the spacing between microtubules from 90 nm to 40 nm. Moreover, there is a decreased number of microtubules in mature MAP2-induced processes whereas in tau and MAP2-induced processes, the number of microtubules is constant along the length. Based on these observations, we conclude that MAP2 isoforms can serve as architectural elements by establishing specific morphological features of processes and specific arrangements of their microtubules.     

Functional equivalence of industrial metal cleaning processes comparison of metal cleaning processes within LCA

In an LCA case study, the three most frequent industrial metal cleaning technologies were assessed: Cleaning based on aqueous cleaning agents, non-halogenated hydrocarbon solvents and halogenated hydrocarbon solvents. Beside optimisation analysis, the comparison of the cleaning processes was a main goal of the study. The function of metal cleaning processes can be described with a set of parameters called functional parameters. In order to compare different cleaning processes within LCA, it is a precondition that all relevant functional parameters be equivalent. However, metal cleaning processes from different companies normally differ in most of the functional parameters and, thus, are not functionally equivalent. Therefore, it is necessary to calculate the material and energy flows of the processes corresponding to a reference function as a basis for comparison. This can be achieved by simulating the processes according to the functional parameters with the help of a process model. For a general comparison of the technologies, it is also necessary to consider the assessed machines having the same level of optimisation and the same scale.     

Rosette glands in the gills of the grass shrimp Palaemonetes pugio. II. Premolt ductule reformation: Replacement of ciliary processes by cytoplasmic processes in relation to gland maturation

The events associated with premolt reformation of the cuticularized ductule in the underdeveloped (immature) branchial rosette glands, which are common in the gills of small (14–18 mm, total length) grass shrimp, are described and contrasted with the events of ductule reformation in the fully developed (mature) resette glands most common in larger shrimp. In immature rosette glands, two ciliary processes emerge from each of the component secretory cells and ascend into the basal luminal region of the old ductule. Subsequently a new ductule is formed around the old ductule, and the ciliary processes disappear, either because of degeneration or retraction. The transitory ciliary processes appear to prevent the old ductule from collapsing during the formation of a new ductule. Such transitory ciliary processes, however, are not found in association with premolt ductule reformation in the mature rosette glands; in their place are seen a number of microvilli-like cytoplasmic processes, which emanate from the apices of the secretory cells and from the channels of the central cell. These cytoplasmic processes in mature glands, like the ciliary processes in immature glands, are transitory and appear to prevent the collapse of the old ductule. Cytoplasmic processes comparable to those in mature glands, but relatively few in number and originating only from the secretory cells, are seen together with ciliary processes in some immature glands. The relative abundance of cytoplasmic processes in the mature glands, coupled with the observation that transitory ciliary processes occur in immature glands but not in mature glands, suggests that, during glandular maturation, transitory ciliary processes are replaced by transitory cytoplasmic processes.     

The oblique muscle organizer in Hirudo medicinalis, an identified embryonic cell projecting multiple parallel growth cones in an orderly array

The oblique muscle layer in the leech body wall is built upon the processes of a unique identified embryonic cell, the Comb- or C-cell. Each C-cell is composed of a spindle-shaped soma that projects approximately 70 parallel processes through the developing body wall at an angle oblique to the long axis. The morphogenesis of this cell and the navigation of its growth cones were examined by intracellular dye filling and antibody staining. At the earliest stages described each C-cell had about six processes, with those near the center of the cell oriented obliquely. As processes were added at the axial ends of the soma they often projected along previously developed longitudinal or circular muscle founder cells and then secondarily aligned themselves parallel to the older processes from the same C-cell. All growth cones initially extended to a particular location in the body wall, where they ceased growing until all 70 processes had been added (over the course of about 5 days). As adjacent segmental homologs met, their growth cones intermingled, eventually sorting out to align parallel. When one of these cells was ablated early--but not later--in development, the remaining adjacent segmental homologs expanded into the vacant territory, consistent with a hypothesis of mutual avoidance between segmental homologs. Most processes that expanded into the experimentally induced vacancy remained correctly oriented and parallel; the few exceptions projected instead along the mirror-image trajectory. Thus, expression of specific avoidance between adjacent C-cell processes is developmentally regulated and functions as a guidance mechanism in vivo, in that it serves to restrict possible trajectories. After aligning its growth cones, each cell stopped adding processes and the processes rapidly extended in concert along relatively precise trajectories. Processes of contralateral homologs cross to form the orthogonal grid used as a scaffold by myocytes to form the oblique muscles. The advancing fronts of growth cones reached the dorsal midline at about the same time as body closure occurs (at about Embryonic Day 20) at which time the C-cells became granular, lost processes, and presumably died. This sequence of developmental events is consistent with temporal and spatial regulation of different morphogenetic strategies, including--but not limited to--specific avoidance, and further suggests testable hypotheses of mechanisms of growth cone navigation in the intact embryo.     

The scale dependence of fungal community distribution in paddy soil driven by stochastic and deterministic processes

Fungal communities play important roles in terrestrial ecosystem functioning. Unraveling the relative importance of stochastic versus deterministic processes in shaping biogeographic patterns of fungal communities has long been a challenge in microbial ecology, owing to high biodiversity and difficulties in identifying fungal taxa. Using a unique anthropogenic system of geographically isolated paddy ‘islands’, we collected 198 soil samples with a spatially explicit design to examine how ecological processes shaped fungal biogeographic patterns. Fungal community structure showed scale-dependent distance-decay relationships. Stochastic processes (dispersal and drift) contributed more to community assembly than deterministic processes (selection) at the local scale, which was largely attributed to drift. In contrast, deterministic processes contributed more to community assembly than stochastic processes at the regional scale, with soil dissolved organic carbon being the most important measured factor. Collectively, scale dependence of fungal biogeographical patterns in paddy soils is influenced by differential contribution of deterministic and stochastic processes.     

Inhibition of a Mitotic Motor Compromises the Formation of Dendrite-like Processes from Neuroblastoma Cells

Microtubules in the axon are uniformly oriented, while microtubules in the dendrite are nonuniformly oriented. We have proposed that these distinct microtubule polarity patterns may arise from a redistribution of molecular motor proteins previously used for mitosis of the developing neuroblast. To address this issue, we performed studies on neuroblastoma cells that undergo mitosis but also generate short processes during interphase. Some of these processes are similar to axons with regard to their morphology and microtubule polarity pattern, while others are similar to dendrites. Treatment with cAMP or retinoic acid inhibits cell division, with the former promoting the development of the axon-like processes and the latter promoting the development of the dendrite-like processes. During mitosis, the kinesin-related motor termed CHO1/MKLP1 is localized within the spindle midzone where it is thought to transport microtubules of opposite orientation relative to one another. During process formation, CHO1/ MKLP1 becomes concentrated within the dendrite-like processes but is excluded from the axon-like processes. The levels of CHO1/MKLP1 increase in the presence of retinoic acid but decrease in the presence of cAMP, consistent with a role for the protein in dendritic differentiation. Moreover, treatment of the cultures with antisense oligonucleotides to CHO1/MKLP1 compromises the formation of the dendrite-like processes. We speculate that a redistribution of CHO1/MKLP1 is required for the formation of dendrite-like processes, presumably by establishing their characteristic nonuniform microtubule polarity pattern.