Minimum evolution using ordinary least-squares is less robust than neighbor-joining

The method of minimum evolution reconstructs a phylogenetic tree T for n taxa given dissimilarity data d. In principle, for every tree W with these n leaves an estimate for the total length of W is made, and T is selected as the W that yields the minimum total length. Suppose that the ordinary least-squares formula S _W (d) is used to estimate the total length of W. A theorem of Rzhetsky and Nei shows that when d is positively additive on a completely resolved tree T, then for all W ≠ T it will be true that S _W (d) > S _T (d). The same will be true if d is merely sufficiently close to an additive dissimilarity function. This paper proves that as n grows large, even if the shortest branch length in the true tree T remains constant and d is additive on T, then the difference S _W (d)-S _T (d) can go to zero. It is also proved that, as n grows large, there is a tree T with n leaves, an additive distance function d _T on T with shortest edge ε, a distance function d, and a tree W with the same n leaves such that d differs from d _T by only approximately ε/4, yet minimum evolution incorrectly selects the tree W over the tree T. This result contrasts with the method of neighbor-joining, for which Atteson showed that incorrect selection of W required a deviation at least ε/2. It follows that, for large n, minimum evolution with ordinary least-squares can be only half as robust as neighbor-joining.     

Survival Chances of Mutants Starting With One Individual

A simple theoretical model of a Darwinian system (a periodic system with a multiplication phase and a selection phase) of entities (initial form of polymer strand, primary mutant and satellite mutants) is given. First case: one mutant is considered. One individual of the mutant appears in the multiplication phase of the first generation. The probabilities to find N mutants W_n^M(N) after the multiplication phase M of the n-th generation (with probability δ of an error in the replication, where all possible errors are fatal errors) and W_n^S(N) after the following selection phase S (with probability β that one individual survives) are given iteratively. The evolutionary tree is evaluated. Averages from the distributions and the probability of extinction W_∞^S(0) are obtained. Second case: two mutants are considered (primary mutant and new form). One individual of the primary mutant appears in the multiplication phase of the first generation. The probabilities to find N_p primary mutants and N_m of the new form W_n^M(N_p, N_m) after the multiplication phase M of the n-th generation (probability ε of an error in the replication of the primary mutant giving the new form) and W_n^S(N_p, N_m) after the following selection phase S (probabilities β_p and β_m that one individual each of the primary mutant and of the new form survives) are given iteratively. Again the evolutionary tree is evaluated. Averages from the distributions are obtained.     

Subthreshold outward currents enhance temporal integration in auditory neurons

Many auditory neurons possess low-threshold potassium currents (I _KLT ) that enhance their responsiveness to rapid and coincident inputs. We present recordings from gerbil medial superior olivary (MSO) neurons in vitro and modeling results that illustrate how I _KLT improves the detection of brief signals, of weak signals in noise, and of the coincidence of signals (as needed for sound localization). We quantify the enhancing effect of I _KLT on temporal processing with several measures: signal-to-noise ratio (SNR), reverse correlation or spike-triggered averaging of input currents, and interaural time difference (ITD) tuning curves. To characterize how I _KLT , which activates below spike threshold, influences a neurons voltage rise toward threshold, i.e., how it filters the inputs, we focus first on the response to weak and noisy signals. Cells and models were stimulated with a computer-generated steady barrage of random inputs, mimicking weak synaptic conductance transients (the noise), together with a larger but still subthreshold postsynaptic conductance, EPSG (the signal). Reduction of I _KLT decreased the SNR, mainly due to an increase in spontaneous firing (more false positive). The spike-triggered reverse correlation indicated that I _KLT shortened the integration time for spike generation. I _KLT also heightened the models timing selectivity for coincidence detection of simulated binaural inputs. Further, ITD tuning is shifted in favor of a slope code rather than a place code by precise and rapid inhibition onto MSO cells (Brand et al. 2002). In several ways, low-threshold outward currents are seen to shape integration of weak and strong signals in auditory neurons.     

幼龄胡杨气孔行为对土壤质地和地下水埋深变化的响应

气孔调节是植物适应水分条件变化的关键途径,研究多变生境中植物气孔行为对认识植物的适应具有重要意义。洪水漫溢新形成的河漫滩是胡杨更新的自然生境,其土壤质地和地下水埋深具高度时空异质性。已有研究主要集中于胡杨对地下水埋深变化的生理生态响应,而对土壤质地与地下水变化交互作用影响植物水分关系的认识不足。通过设置土壤质地(砂土(S₁)、砂壤土(S₂)、黏壤土(S₃)与地下水埋深(W₁(30 cm)、W₂(60 cm)、W₃(90 cm))交互试验模拟幼龄胡杨自然生境,观测分析了不同条件下胡杨气孔导度(G_s)、气孔导度斜率(g₁)、光合的气孔限制(L_s)的变化。研究结果表明：(1)胡杨气孔行为对地下水变化的响应受土壤质地影响;(2)相同地下水埋深时不同土质间G_s具显著差异,W₁时S₂与S₃的G_s...     

A note on the excitation of nerve pathways

LetS denote the intensity of a stimulus, ν the frequency of discharge of a fiber, and ν _T the integral frequency of discharge of a nerve pathway. The relation between ν _T andS can be derived when the relation between ν andS, as well as the distribution function of the fiber thresholds are given. It is investigated under what conditions the functions ν _T (S) and ν(s) will be both of the same exponential form, and it is shown that this can happen only ifS exceeds the highest threshold of the pathway.     

Analysis of microsomal flavoproteins from Phycomyces sporangiophores: Candidates for the blue-light photoreceptor

To help identify components of the blue-light photoreceptor system for phototropism in Phycomyces blakesleeanus Bgff., proteins from a microsomal fraction obtained from synchronous sporangiophores were studied. By two-dimensional gel electrophoresis, two proteins (FP₁, FP₂) with covalently bound flavins were found. FP₁ has a molecular weight of 71 000 and an isoelectric point of 6.6; FP₂ has a molecular weight of 59 000 and an isoelectric point of 6.5. These flavoproteins were purified by column chromatography and gel filtration while assaying for flavins by fluorescence. The relative concentrations of FP₁ and FP₂ were affected by light applied during growth. These flavoproteins are likely components of the blue-light photoreceptor complex mediating phototropism in Phycomyces.Abbreviations 10 k pellet 10 000-g pellet - 100 k pellet 100 000-g pellet - FP₁, FP₂ proteins with covalently bound flavins having molecular weights of 71 000 and 59 000 and isoelectric points of 6.6 and 6.5, respectively     

Spike-Frequency Adaptation of a Generalized Leaky Integrate-and-Fire Model Neuron

Although spike-frequency adaptation is a commonly observed property of neurons, its functional implications are still poorly understood. In this work, using a leaky integrate-and-fire neural model that includes a Ca²⁺-activated K⁺ current (I _AHP), we develop a quantitative theory of adaptation temporal dynamics and compare our results with recent in vivo intracellular recordings from pyramidal cells in the cat visual cortex. Experimentally testable relations between the degree and the time constant of spike-frequency adaptation are predicted. We also contrast the I _AHP model with an alternative adaptation model based on a dynamical firing threshold. Possible roles of adaptation in temporal computation are explored, as a a time-delayed neuronal self-inhibition mechanism. Our results include the following: (1) given the same firing rate, the variability of interspike intervals (ISIs) is either reduced or enhanced by adaptation, depending on whether the I _AHP dynamics is fast or slow compared with the mean ISI in the output spike train; (2) when the inputs are Poisson-distributed (uncorrelated), adaptation generates temporal anticorrelation between ISIs, we suggest that measurement of this negative correlation provides a probe to assess the strength of I _AHP in vivo; (3) the forward masking effect produced by the slow dynamics of I _AHP is nonlinear and effective at selecting the strongest input among competing sources of input signals.     

Maturation of GABAergic Inhibition Promotes Strengthening of Temporally Coherent Inputs among Convergent Pathways

Spike-timing-dependent plasticity (STDP), a form of Hebbian plasticity, is inherently stabilizing. Whether and how GABAergic inhibition influences STDP is not well understood. Using a model neuron driven by converging inputs modifiable by STDP, we determined that a sufficient level of inhibition was critical to ensure that temporal coherence (correlation among presynaptic spike times) of synaptic inputs, rather than initial strength or number of inputs within a pathway, controlled postsynaptic spike timing. Inhibition exerted this effect by preferentially reducing synaptic efficacy, the ability of inputs to evoke postsynaptic action potentials, of the less coherent inputs. In visual cortical slices, inhibition potently reduced synaptic efficacy at ages during but not before the critical period of ocular dominance (OD) plasticity. Whole-cell recordings revealed that the amplitude of unitary IPSCs from parvalbumin positive (Pv+) interneurons to pyramidal neurons increased during the critical period, while the synaptic decay time-constant decreased. In addition, intrinsic properties of Pv+ interneurons matured, resulting in an increase in instantaneous firing rate. Our results suggest that maturation of inhibition in visual cortex ensures that the temporally coherent inputs (e.g. those from the open eye during monocular deprivation) control postsynaptic spike times of binocular neurons, a prerequisite for Hebbian mechanisms to induce OD plasticity.     

On the integration of subthreshold inputs from Perforant Path and Schaffer Collaterals in hippocampal CA1 pyramidal neurons

Using a realistic model of a CA1 hippocampal pyramidal neuron, we make experimentally testable predictions on the roles of the non-specific cation current, I _h , and the A-type Potassium current, I _A , in modulating the temporal window for the integration of the two main excitatory afferent pathways of a CA1 neuron, the Schaffer Collaterals and the Perforant Path. The model shows that the experimentally observed increase in the dendritic density of I _h and I _A could have a major role in constraining the temporal integration window for these inputs, in such a way that a somatic action potential (AP) is elicited only when they are activated with a relative latency consistent with the anatomical arrangement of the hippocampal circuitry.     

Primary genome scan for complex body shape‐related traits in the common carp Cyprinus carpio

To identify quantitative trait loci (QTL) that affect body shape in common carp Cyprinus carpio, a linkage map, 2159·23 cM long, was constructed with a total of 307 markers covering 51 linkage groups (LG). The map included 167 new single nucleotide polymorphism (SNP) markers derived from expressed sequence tags (EST) together with 140 microsatellite markers reported earlier. A primary genome scan was conducted for QTL for standard length (L_S), head length (L_H), body height (H_B), body width (W_B) and tail length (L_TAIL) in an F1 line containing 92 offspring. A total of 15 suggestive QTL on six LGs were found to associate with L_S, L_H, H_B, W_B and L_TAIL which explained 10·7–17·4% of the variance. Five significant QTL were detected for body‐shape related traits and located for LGs (lg1, 12 and 20). These QTL included: one associated with L_S (21·1% variance explained), three for H_B (almost 20% variance explained) and one for W_B (20·7% variance explained).     

Evaluation of the Fermi equation as a model of dose-response curves

 When plotted in linear coordinates, the dose-response curves of microorganisms exposed to a lethal agent, such as radiation or a toxic substance, often have a characteristic sigmoid shape. Irrespective of whether they are very narrow or broad they can be described by the Fermi function, which is a mirror image of the logistic function, i.e. S(X)=1/{1+ exp [(X−X _c)/a]} where S(X) is the fraction of the surviving organisms, X the dose of the lethal agent, X _c a characteristic dose marking the inflection point of S(X), which corresponds to 50% mortality, and a a measure of the steepness of the survival curve around X _c. It is demonstrated that, if the susceptibilities of the individual organisms, expressed in terms of a characteristic lethal dose, have a symmetric unimodal distribution, the dose-response curve of the population has a Fermian sigmoid shape. It is also shown that the mode and variance of the distribution can be estimated from the shape parameters of the Fermian survival curve, X _c and a. Received: 7 November 1995 / Received last revision: 11 April 1996 / Accepted: 29 April 1996     

Adsorption Characteristics and the Effect of Dissolved Organic Matter on Mercury(II) Adsorption of Various Soils in China

To evaluate the adsorption characteristics and effects of dissolved organic matter (DOM) from wheat straw (DOM_W) and swine manure (DOM_S) on mercury [Hg(II)] adsorption by soils, a series of experiments was conducted on 26 soils with different soil properties.Results showed that the values of K_d (a solid–liquid partition coefficient) of soils varied within a range of 0.768–14.386 L g^?1. K_d values were mainly controlled by soil organic matter (SOM), cation exchange capacity (CEC), soil nitrogen (N), and soil sulfur (S). When DOM_W and DOM_S were added to the soil samples, the amount of Hg(II) adsorbed by the soils decreased significantly. Furthermore, based on the decreased percentage of adsorption of Hg(II) by soil upon adding DOM_W (P_DOMW) or DOM_S (P_DOMS), about 73.08% soils, the values of P_DOMS were smaller than those of P_DOMW. The P_DOMW values were related to SOM, pH, free Fe oxide content, and CEC, whereas P_DOMS values were related to soil free Fe/Al oxide contents. Therefore, we should pay more attention about mercury risk caused by the addition of exogenous organic matter in soils, especially for the soils with low or high pH, less SOM, low CEC, and less free Fe/Al oxide.     

A comparison of the Schumacher with other functions for describing growth in pigs

This study was undertaken to introduce the Schumacher equation and compare it with established functions for describing growth in pigs. The relationship between live weight (LW) and cumulative feed intake was also investigated. A database was constructed from three independent trials in which LW, age and intake were measured from birth to 937 days. Three growth functions were used for analysis of growth versus age: Gompertz, Schumacher and Weibull; and the Richards and monomolecular equations were used for analysis of cumulative feed intake versus LW. The growth functions have different points of inflexion. Liveweight at inflexion is W_f/e for the Gompertz, where W_f is the final weight, W_f/e² for the Schumacher, and W_f − (W_f − W₀) exp[−(n − 1)/n] for the Weibull, where W₀ is initial body weight and n is a shape parameter. Meta-analysis of the data using mixed model and nonlinear regression procedures was conducted to identify the most appropriate growth function. Functions were compared using F-tests or Bayesian Information Criteria, which give a value based on best fit and number of parameters in the model. The three equations were fitted to five individual pig growth profiles and to the composite data. Although the Weibull had a lower residual mean square, it did not significantly improve the fit compared to the simpler models and appears to be over-parameterised. The results suggest that model selection should be based on the type and amount of data available for analysis. Residuals plot showed that Schumacher and Weibull better predict the initial growth phase, however, all models showed largest magnitude of residuals towards the end of the growth profile. The monomolecular equation was most appropriate for describing LW against cumulative feed intake and may be used to formulate diets based on the efficiency of conversion of feed to LW at various stages of the animal's life span.     

Current noise generated by electrogenic ion pumps

Active ion transport by ATP-or light-driven pumps involves a sequence of elementary steps such as binding and release of ions, as well as conformational transitions of the pump protein. At the microscopic level the individual reaction steps occur at random intervals, and therefore the current generated by electrogenic pumps fluctuates around a mean value. In this paper, a theoretical treatment of the electrical noise associated with active ion transport is given. The analysis, which is based on the calculation of the correlation function, yields the spectral intensity S ₁ of current noise as a function of frequency, f. The shape of S _I(f) contains information on the rate constants as well as on the magnitude of the charge displacements occuring during single reaction steps. The contribution of electrogenic pumps to the total voltage noise of the cell may be estimated from S _I(f) and from the frequency-dependent impedance of the cell membrane.     

Phycomyces: a new gene for a flavoprotein with covalently linked cofactor

Summary We have identified a new locus in Phycomyces blakesleeanus that codes for a flavoprotein designated previously as FP₂. According to results from a sexual cross, this locus, flp, maps near the gene madC, a marker for abnormal phototropic sensitivity. The recombination frequency between flp and madC is about 10%. Further, the flp marker is unlinked with the carotene locus carA. Because the flavoprotein FP₂ is absent in certain photoreceptor mutants (Pollock et al. 1985 a), it had been proposed as a candidate for the blue-light photoreceptor. We have found, however, that some strains lacking this protein retain normal phototropism. Therefore, the flavoprotein FP₂ is probably not involved in photoreception.     

Relationship between specific leaf area of aCryptomeria japonica foliage shoot segment and its diameter

Dependency of specific leaf area (SLA) on shoot diameter (x) was studied forCryptomeria japonica foliage shoot segments about 5 cm in length taken from 18 branches at different height levels on 3 trees in August 1987. The leaf area of a shoot segment (S) was defined as half the sum of the needle area (s) estimated by the allometric relationship betweens and needle length. The dry weight of woody tissue (W _w) and needles (W _n) of a segment and itsS were divided by the segment length (L) to give linear densities asW _w/L,W _n/L andS/L, respectively. The densities were related tox by power-form equations.S/L values tended to be constant around 1.2 [cm² cm⁻¹] within the discussed range ofx, whileW _w/L andW _n/L values clearly increased withx. The approximately reciprocal relationship between average needle area (s) and linear density of the number of needles supported the fact thatS/L values were roughly constant regardless ofx.SLA andSNA were defined asS/(W _w+W _n) andS/W _n, respectively. TheSLA-x relationship expected from the average value ofS/L and theW _w/L-x and theW _n/L-x relationships was well fitted to the observed decrease inSLA with increasingx. SNA also decreased asx increased. Variations inSLA andSNA among the shoot segments with similarx were not systematically related to their height levels. An empirical equation with a maximum value ofx (Xmax) was also proposed in order to formulate theSLA-x relationship.     

神经元放电阈值的可变性及其意义

神经元能够将不同时空模式的突触输入转化为时序精确的动作电位输出，这种灵活、可靠的信息编码方式是神经集群在动态环境或特定任务下产生所需活动模式的重要基础。动作电位的产生遵循全或无规律，只有当细胞膜电压达到放电阈值时，神经元才产生动作电位。放电阈值在细胞内和细胞间具有高度可变性，具体动态依赖于刺激输入和放电历史。特别是，放电阈值对动作电位起始前的膜电压变化十分敏感，这种状态依赖性产生的生物物理根源包括Na⁺失活和K⁺激活。在绝大多数神经元中，动作电位的触发位置是轴突起始端，这个位置处的阈值可变性是决定神经元对时空输入转化规律的关键因素。但是，电生理实验中动作电位的记录位置却通常是胞体或近端树突，此处的阈值可变性高于轴突起始端，而其产生的重要根源是轴突动作电位的反向传播。基于胞体测量的相关研究显示，放电阈值动态能够增强神经元的时间编码、特征选择、增益调控和同时侦测能力。本文首先介绍放电阈值的概念及量化方法，然后详细梳理近年来国内外关于放电阈值可变性及产生根源的研究进展，在此基础上归纳总结放电阈值可变性对神经元编码的重要性，最后对未来放电阈值的研究方向进行展望。     

Why spikes? Hebbian learning and retrieval of time-resolved excitation patterns

Hebbian learning allows a network of spiking neurons to store and retrieve spatio-temporal patterns with a time resolution of 1 ms, despite the long postsynaptic and dendritic integration times. To show this, we introduce and analyze a model of spiking neurons, the spike response model, with a realistic distribution of axonal delays and with realistic postsynaptic potentials. Learning is performed by a local Hebbian rule which is based on the synchronism of presynaptic neurotransmitter release and some short-acting postsynaptic process. The time window of this synchronism determines the temporal resolution of pattern retrieval, which can be initiated by applying a short external stimulus pattern. Furthermore, a rate quantization is found in dependence upon the threshold value of the neurons, i.e., in a given time a pattern runsn times as often as learned, wheren is a positive integer (n 0). We show that all information about the spike pattern is lost if only mean firing rates (temporal average) or ensemble activities (spatial average) are considered. An average over several retrieval runs in order to generate a post-stimulus time histogram may also deteriorate the signal. The full information on a pattern is contained in the spike raster of a single run. Our results stress the importance, and advantage, of coding by spatio-temporal spike patterns instead of firing rates and average ensemble activity. The implications regarding modelling and experimental data analysis are discussed.     

Relationship between surplus energy and body weight in fish populations

This paper theoretically analyses the relationship between surplus energy, which is available for either somatic growth or reproduction, and body weight. From the data of metabolism and growth of the biwamasu, Oncorhynchus rhodurus, obtained by Miura et al., a Bernoulli's differential equation is induced to represent the relationship between body weight and the sum of surplus energy and active metabolic rate. Solving this equation gives the amount of surplus energy, f(W_x), as follows:f(W_x) = (αW_x^1−γ+β^1−γ)^1/(1−γ)−W_x, in which α, β and γ are constants and W_x is body weight at age x. The function is applied to ten fish populations and consequently it is found to be useful for a wider age range and a wider variety of fishes than the conventional function.     

Effects of environmental synchrony and density-dependent dispersal on temporal and spatial slopes of Taylor's law

Taylor's law (TL) is an empirical rule that describes an approximate relationship between the variance and mean of population density: log₁₀(variance) ≈ log₁₀(a) + b × log₁₀(mean). Population synchrony is another prevailing feature observed in empirical populations. This study investigated the effects of environmental synchrony and density-dependent dispersal on the temporal (b_T) and spatial (b_S) slopes of TL, using an empirical dataset of gray-sided vole populations and simulation analyses based on the second-order autoregressive (AR) model. Eighty-five empirical populations satisfied the temporal and spatial TLs with b_T = 1.943 (±SE 0.143) and b_S = 1.579 (±SE 0.136). The pairwise synchrony of population was 0.377 ± 0.199 (mean ± SD). Most simulated populations that obeyed the AR model satisfied the form of the temporal and spatial TLs without being affected by the environmental synchrony and density-dependent dispersal; however, those simulated slopes were too steep. The incorporation of environmental synchrony resulted in reduced simulated slopes, but those slopes, too, were still unrealistically steep. By incorporating density-dependent dispersal, simulated slopes decreased and fell within a realistic range. However, the simulated populations without environmental synchrony did not exhibit an adequate degree of density synchrony. In simulations that included both environmental synchrony and density-dependent dispersal, 92.7% of the simulated datasets provided realistic values for b_T, b_S and population synchrony. Because the two slopes were more sensitive to the variation of density-dependent dispersal than that of environmental synchrony, density-dependent dispersal may be the key to the determination of b_T and b_S.