生物多样性数据集成模式初探

本文以生物多样性研究发展现状的分析为基础,为生物多样性保护政策的制定提供可靠的数据支持为目标,通过对国内外几个著名的生物多样性数据库建设情况的分析,从相关学者的需求出发,提出了设计一个多层次多角度并带有一定人工智能的生物多样性集成数据库的构想。该系统基于都柏林核心(Dublin Core)的数据规范,并符合基于开放文献预研的元数据互操作协议(The Open Archixles Initiative Protocol for Metadata Hatvesting,OAIPMH)的标准,是一个集文字、图件、图片、声音、影像为一体的,能够在网上和硬件载体(如光盘)上同时进行发布的分布式数据库平台。其网上数据库系统的子系统之间以及子系统和硬件载体之间可以通过元数据获取的开放档案倡议协议互相交换数据。     

Energy detection and temporal integration in the noctuid A1 auditory receptor

The temporal integration of the A1 auditory receptor of two species of noctuid moths (Lepidoptera, Noctuidae) was investigated. Tympanal nerve spikes were recorded while stimulating the ear with broad band clicks. Thresholds were measured for single clicks, pairs of clicks with a separation of 1–20 ms, and trains of up to 8 clicks at separations of 1–2 ms. The average threshold for single clicks was 52.9 dB peSPL (SD 1.7 dB, n = 40) for Noctua pronuba and 50.1 dB peSPL (SD 4.0 dB, n = 27) for Spodoptera littoralis. The thresholds for double clicks with a 1 ms separation were lower than the thresholds for single clicks. The difference decreased as the separation between the clicks was increased. The results were fully consistent with an energy detector model (a leaky integrator with an exponential decay) with a time constant of about 4 ms.The results are compared to previously published results with pure tone intensity/duration trading. A common underlying mechanism is suggested, based on the passive electric properties of the receptor cell membrane.It is suggested, that the time constant revealed in the present study characterizes auditory receptors in general, and is related to the short time constants in vertebrate audition.Abbreviations peSPL peak equivalent sound pressure level - SD standard deviation - time constant     

The effect of temporal variability on persistence conditions in rivers

There has been great interest in the invasion and persistence of algal and insect populations in rivers. Recent modeling approaches assume that the flow speed of the river is constant. In reality, however, flow speeds in rivers change significantly on various temporal scales due to seasonality, weather conditions, or many human activities such as hydroelectric dams. In this paper, we study persistence conditions by deriving the upstream invasion speed in simple reaction-advection-diffusion equations with coefficients chosen to be periodic step functions. The key methodological idea to determine the spreading speed is to use the exponential transform in order to obtain a moment generating function. In a temporally periodic environment, the averages of each coefficient function determine the minimal upstream and downstream propagation speeds for a single-compartment model. For a two-compartment model, the temporal variation can enhance population persistence.     

Composite temporal strategies in pathogen evolution: balancing invasion and persistence

There is ongoing interest in the conditions that favor the evolution of acute, highly transmissible infections in contrast to chronic ones. Earlier studies typically consider the evolution of a trait that is constant over the lifetime of an infection. However, for many pathogens, such traits can vary over this course. Here, we address the evolution of temporal patterns in limited host population sizes, where a trade-off between invasion and persistence can arise. This is of particular relevance to questions on the evolution of acuteness and chronicity. We ask whether population dynamics of transmission at the between-host level could lead pathogen adaptation to favor temporal strategies during the course of infection. To do this, we consider an infection to be composed of multiple stages, allowing each of these to evolve independently under a transmission–duration trade-off. We only consider selection taking place on the between-host level and examine the balance of invasion and persistence (i.e., maximizing replication vs. minimizing vulnerability to extinction), using several fitness-related measures. We find that a composite strategy that is ordered in time can confer higher fitness than any single, constant, strategy. We discuss the relevance of these results for the ordered expression of var genes in Plasmodium falciparum, as well as for infections that characteristically have several stages as in some bacterial pathogens.     

A neurocomputational model for optimal temporal processing

Humans can estimate the duration of intervals of time, and psychophysical experiments show that these estimations are subject to timing errors. According to standard theories of timing, these errors increase linearly with the interval to be estimated (Weber's law), and both at longer and shorter intervals, deviations from linearity are reported. This is not easily reconciled with the accumulation of neuronal noise, which would only lead to an increase with the square root of the interval. Here, we offer a neuronal model which explains the form of the error function as a result of a constrained optimization process. The model consists of a number of synfire chains with different transmission times, which project onto a set of readout neurons. We show that an increase in the transmission time corresponds to a superlinear increase of the timing errors. Under the assumption of a fixed chain length, the experimentally observed error function emerges from optimal selection of chains for each given interval. Furthermore, we show how this optimal selection could be implemented by competitive spike-timing dependent plasticity in the connections from the chains to the readout network, and discuss implications of our model on selective temporal learning and possible neural architectures of interval timing.     

A multisensory integration model of human stance control

A model is presented to study and quantify the contribution of all available sensory information to human standing based on optimal estimation theory. In the model, delayed sensory information is integrated in such a way that a best estimate of body orientation is obtained. The model approach agrees with the present theory of the goal of human balance control. The model is not based on purely inverted pendulum body dynamics, but rather on a three-link segment model of a standing human on a movable support base. In addition, the model is non-linear and explicitly addresses the problem of multisensory integration and neural time delays. A predictive element is included in the controller to compensate for time delays, necessary to maintain erect body orientation. Model results of sensory perturbations on total body sway closely resemble experimental results. Despite internal and external perturbations, the controller is able to stabilise the model of an inherently unstable standing human with neural time delays of 100 ms. It is concluded, that the model is capable of studying and quantifying multisensory integration in human stance control. We aim to apply the model in (1) the design and development of prostheses and orthoses and (2) the diagnosis of neurological balance disorders. Received: 25 August 1997 / Accepted in revised form: 8 December 1998     

A model for neural representation of temporal duration

To address how temporal duration is encoded in neural systems, we put forward a simple model for recurrent neural networks. Particular assumptions are only the following two: (1) neuronal bistability and; (2) environmental effects described by a heat bath. The results of Monte Carlo simulation show that population activity triggered at an initial time continues for a prolonged duration, followed by an abrupt self-termination. This time course seems highly suitable for neural representation of temporal duration. The time scale of this prolonged duration is much longer than the time scale of neuronal firing which is of the order of ms. The former time scale implies that of interval timing in cognition and behaviour. Thus, the model provides a possible explanation for a link between these two separated time scales. The Weber law, a hallmark of humans and animals' interval timing, can also be reproduced in our model.     

A competitive integration model of exogenous and endogenous eye movements

We present a model of the eye movement system in which the programming of an eye movement is the result of the competitive integration of information in the superior colliculi (SC). This brain area receives input from occipital cortex, the frontal eye fields, and the dorsolateral prefrontal cortex, on the basis of which it computes the location of the next saccadic target. Two critical assumptions in the model are that cortical inputs are not only excitatory, but can also inhibit saccades to specific locations, and that the SC continue to influence the trajectory of a saccade while it is being executed. With these assumptions, we account for many neurophysiological and behavioral findings from eye movement research. Interactions within the saccade map are shown to account for effects of distractors on saccadic reaction time (SRT) and saccade trajectory, including the global effect and oculomotor capture. In addition, the model accounts for express saccades, the gap effect, saccadic reaction times for antisaccades, and recorded responses from neurons in the SC and frontal eye fields in these tasks.     

Dendritic network structure and dispersal affect temporal dynamics of diversity and species persistence

Landscape connectivity structure, specifically the dendritic network structure of rivers, is expected to influence community diversity dynamics by altering dispersal patterns, and subsequently the unfolding of species interactions. However, previous comparative and experimental work on dendritic metacommunities has studied diversity mostly from an equilibrium perspective. Here we investigated the effect of dendritic versus linear network structure on local (α‐diversity), among (β‐diversity) and total (γ‐diversity) temporal species community diversity dynamics. Using a combination of microcosm experiments, which allowed for active dispersal of 14 protists and a rotifer species, and numerical analyses, we demonstrate the general importance of spatial network configuration and basic life history tradeoffs as driving factors of different diversity patterns in linear and dendritic systems. We experimentally found that community diversity patterns were shaped by the interaction of dispersal within the networks and local species interactions. Specifically, α‐diversity remained higher in dendritic networks over time, especially at highly connected sites. β‐diversity was initially greater in linear networks, due to increased dispersal limitation, but became more similar to β‐diversity in dendritic networks over time. Comparing the experimental results with a neutral metacommunity model we found that dispersal and network connectivity alone may, to a large extent, explain α‐ and β‐diversity dynamics. However, additional mechanisms, such as variation in carrying capacity and competition–colonization tradeoffs, were needed in the model to capture the detailed temporal diversity dynamics of the experiments, such as a general decline in γ‐diversity and long‐term dynamics in α‐diversity.     

Effects of temporal variability on rare plant persistence in annual systems

Traditional conservation biology regards environmental fluctuations as detrimental to persistence, reducing long-term average growth rates and increasing the probability of extinction. By contrast, coexistence models from community ecology suggest that for species with dormancy, environmental fluctuations may be essential for persistence in competitive communities. We used models based on California grasslands to examine the influence of interannual fluctuations in the environment on the persistence of rare forbs competing with exotic grasses. Despite grasses and forbs independently possessing high fecundity in the same types of years, interspecific differences in germination biology and dormancy caused the rare forb to benefit from variation in the environment. Owing to the buildup of grass competitors, consecutive favorable years proved highly detrimental to forb persistence. Consequently, negative temporal autocorrelation, a low probability of a favorable year, and high variation in year quality all benefited the forb. In addition, the litter produced by grasses in a previously favorable year benefited forb persistence by inhibiting its germination into highly competitive grass environments. We conclude that contrary to conventional predictions of conservation and population biology, yearly fluctuations in climate may be essential for the persistence of rare species in invaded habitats.     

A model of tenascin-X integration within the collagenous network

Tenascin-X is an extracellular matrix protein whose absence leads to an Ehlers-Danlos syndrome in humans, characterized mainly by disorganisation of collagen and elastic fibril networks. After producing recombinant full-length tenascin-X in mammalian cells, we find that this protein assembled into disulfide-linked oligomers. Trimers were the predominant form observed using rotary shadowing. By solid phase interaction studies, we demonstrate that tenascin-X interacts with types I, III and V fibrillar collagen molecules when they are in native conformation. The use of tenascin-X variants with large regions deleted indicated that both epidermal growth factor repeats and the fibrinogen-like domain are involved in this interaction. Moreover, we demonstrate that tenascin-X binds to the fibril-associated types XII and XIV collagens. We thus suggest that tenascin-X, via trimerization and multiple interactions with components of collagenous fibrils, plays a crucial role in the organisation of extracellular matrices.     

A model of Helicobacter pylori persistence in a case of gastric cancer

The aim of this work was to analyze several clones of Helicobacter pylori isolated from a patient with gastric cancer, to evaluate i) genetic variability ii) virulence factors profile and iii) antimicrobial susceptibility against the drugs commonly used in the H. pylori therapy. A total of 32 H. pylori clones isolated from a biopsy sample coming from a patient with gastric cancer previously treated for H. pylori infection, were analyzed for: the genetic variability by amplified fragment polymorphism analysis; the vacA, cagA virulence status by PCR; the antimicrobial susceptibility by minimum inhibitory concentrations with the agar dilution method towards amoxicillin, clarithromycin, levofloxacin and tinidazole. The patient showed a mixed infection with the presence of at least 3 different strains. The clones isolated possessed the vacA, cagA virulence factors with a different allelic combination (vacA s1/i1/m1; s1/i1i2/m1; s2/i2/m2; s2/i1i2/m2) together with repeated cagA EPIYA motif pattern P1P2P3P3P3. Moreover, a pattern of multi-drug resistance was disclosed in the different clones. The presence of multiple H. pylori strains colonizing the same patient, with the main virulence factors displaying a different allelic combination and a different multi-drug resistance among isolates, point out the role of genetic variability generating, in time, more virulent and adapted strains.     

A discrete-time model for population persistence in habitats with time-varying sizes

Journal of Mathematical Biology - In this paper, we use periodic and stochastic integrodifference models to study the persistence of a single-species population in a habitat with temporally varying...     

A cross-interval spike train analysis: the correlation between spike generation and temporal integration of doublets

A stochastic spike train analysis technique is introduced to reveal the correlation between the firing of the next spike and the temporal integration period of two consecutive spikes (i.e., a doublet). Statistics of spike firing times between neurons are established to obtain the conditional probability of spike firing in relation to the integration period. The existence of a temporal integration period is deduced from the time interval between two consecutive spikes fired in a reference neuron as a precondition to the generation of the next spike in a compared neuron. This analysis can show whether the coupled spike firing in the compared neuron is correlated with the last or the second-to-last spike in the reference neuron. Analysis of simulated and experimentally recorded biological spike trains shows that the effects of excitatory and inhibitory temporal integration are extracted by this method without relying on any subthreshold potential recordings. The analysis also shows that, with temporal integration, a neuron driven by random firing patterns can produce fairly regular firing patterns under appropriate conditions. This regularity in firing can be enhanced by temporal integration of spikes in a chain of polysynaptically connected neurons. The bandpass filtering of spike firings by temporal integration is discussed. The results also reveal that signal transmission delays may be attributed not just to conduction and synaptic delays, but also to the delay time needed for temporal integration. Received: 3 March 1997 / Accepted in revised form: 6 November 1997     

Deficit in visual temporal integration in autism spectrum disorders

Individuals with autism spectrum disorders (ASD) are superior in processing local features. Frith and Happe conceptualize this cognitive bias as ‘weak central coherence’, implying that a local enhancement derives from a weakness in integrating local elements into a coherent whole. The suggested deficit has been challenged, however, because individuals with ASD were not found to be inferior to normal controls in holistic perception. In these opposing studies, however, subjects were encouraged to ignore local features and attend to the whole. Therefore, no one has directly tested whether individuals with ASD are able to integrate local elements over time into a whole image. Here, we report a weakness of individuals with ASD in naming familiar objects moved behind a narrow slit, which was worsened by the absence of local salient features. The results indicate that individuals with ASD have a clear deficit in integrating local visual information over time into a global whole, providing direct evidence for the weak central coherence hypothesis.     

A unified model for the combined temporal and spatial Broca-Sulzer effect

A briefly pulsed light is brighter than a pulse of longer duration. For a brief flash of fixed duration and small area, enlarging a target results initially in an increase in brightness. Beyond some critical area, the target dims with further increases in size. These two phenomena are the temporal and the spatial Broca-Sulzer effect respectively. Each effect can be modeled using a generalization of the Hartline-Ratliff equation. The resulting analysis produces a mathematically unified treatment of both effects.     

A型肉毒毒素轻链胞内持留模型的建立

[目的] 建立A型肉毒毒素轻链胞内持留模型来模拟A型肉毒毒素引起的长期中毒。[方法] 设计构建pcDNA3.1-ALC-GFP重组质粒,提取质粒进行PCR验证,并将其转染进Nureo-2a细胞中表达,利用Western Blot与细胞免疫荧光分析验证ALC-GFP的表达情况及其在细胞内的长时间持留,建立A型肉毒毒素轻链的胞内持留模型,并将该模型用于抗肉毒药物的筛选。[结果] 成功构建pcDNA3.1-ALC-GFP重组质粒并将其转染进Nureo-2a细胞中,验证了ALC-GFP在细胞内具有长时间持留性,成功建立了A型肉毒毒素轻链胞内持留模型,并利用该模型筛选出潜在抗肉毒药物CB3。[结论] 成功建立了A型肉毒毒素轻链胞内持留模型,并初步应用于CS1,CE2和CB3药物筛选,为A型肉毒毒素长期中毒的解毒研究奠定了基础。