Facilitatory and inhibitory effects of blocked-trial fixation of the target location on a chimpanzee's (Pan troglodytes) visual search performance

During a visual search performance by a chimpanzee (Pan troglodytes), horizontal location (column) of target was sequentially changed across 48-trial blocks. Reaction time was used for measure of facilitatory and inhibitory effects of the blocked-trial fixation on her search performance. The chimpanzee showed significant decrease of response time in the later phase of each block in comparison with the condition in which the target location was changed to another column than before changing. Furthermore, difference in response time before and after changing column monotonically and linearly increased as a function of distance between columns. In summary, the blocked-trial fixation of the target location facilitated the chimpanzee's visual-search performance, and that when the pretrial information became invalid, her performance was clearly disrupted. Pretrial information about target location could “prime” and modify the chimpanzee's search strategy.     

Motif frequency and evolutionary search times in RNA populations

RNA molecules, through their dual identity as sequence and structure, are an appropriate experimental and theoretical model to study the genotype-phenotype map and evolutionary processes taking place in simple replicator populations. In this computational study, we relate properties of the sequence-structure map, in particular the abundance of a given secondary structure in a random pool, with the number of replicative events that an initially random population of sequences needs to find that structure through mutation and selection. For common structures, this search process turns out to be much faster than for rare structures. Furthermore, search and fixation processes are more efficient in a wider range of mutation rates for common structures, thus indicating that evolvability of RNA populations is not simply determined by abundance. We also find significant differences in the search and fixation processes for structures of same abundance, and relate them with the number of base pairs forming the structure. Moreover, the influence of the nucleotide content of the RNA sequences on the search process is studied. Our results advance in the understanding of the distribution and attainability of RNA secondary structures. They hint at the fact that, beyond sequence length and sequence-to-function redundancy, the mutation rate that permits localization and fixation of a given phenotype strongly depends on its relative abundance and global, in general non-uniform, distribution in sequence space.     

Human visual search does not maximize the post-saccadic probability of identifying targets

Researchers have conjectured that eye movements during visual search are selected to minimize the number of saccades. The optimal Bayesian eye movement strategy minimizing saccades does not simply direct the eye to whichever location is judged most likely to contain the target but makes use of the entire retina as an information gathering device during each fixation. Here we show that human observers do not minimize the expected number of saccades in planning saccades in a simple visual search task composed of three tokens. In this task, the optimal eye movement strategy varied, depending on the spacing between tokens (in the first experiment) or the size of tokens (in the second experiment), and changed abruptly once the separation or size surpassed a critical value. None of our observers changed strategy as a function of separation or size. Human performance fell far short of ideal, both qualitatively and quantitatively.     

The timing of sequences of saccades in visual search

According to the LATER model (linear approach to thresholds with ergodic rate), the latency of a single saccade in response to target appearance can be understood as a decision process, which is subject to (i) variations in the rate of (visual) information processing; and (ii) the threshold for the decision. We tested whether the LATER model can also be applied to the sequences of saccades in a multiple fixation search, during which latencies of second and subsequent saccades are typically shorter than that of the initial saccade. We found that the distributions of the reciprocal latencies for later saccades, unlike those of the first saccade, are highly asymmetrical, much like a gamma distribution. This suggests that the normal distribution of the rate r, which the LATER model assumes, is not appropriate to describe the rate distributions of subsequent saccades in a scanning sequence. By contrast, the gamma distribution is also appropriate to describe the distribution of reciprocal latencies for the first saccade. The change of the gamma distribution parameters as a function of the ordinal number of the saccade suggests a lowering of the threshold for second and later saccades, as well as a reduction in the number of target elements analysed.     

The consequences of partially directed search effort

Search effort is undirected when a forager has a stereotypical searching behaviour that results in fixed encounter rates with its prey (e.g. diet choice models), and is directed when the forager can bias its encounter with a ‘chosen’ prey. If the bias is complete, search is totally directed (e.g. habitat selection models). When the bias is incomplete (i.e. search modes are not exclusive to a single prey type), search is partially directed. The inclusion of a prey type in the diet is then the result of two decisions: (1) which prey to search for and (2) which prey to handle. The latter decision is determined by the ratio of energy to handling time and the abundance of the preferred prey. The former decision is a function of the encounter probabilities and densities of all potential prey types in addition to their ratio of energy to handling time. Assuming two prey types, there are three distinct behavioural strategies: (1) search for the preferred prey/forage selectively; (2) search for the preferred prey/forage opportunistically; and (3) search for the non-preferred prey/forage opportunistically. If prey are depletable (i.e. prey occur in resource patches), the forager may switch search modes such that prey are depleted to the point where the marginal values of the search modes are equalized. This revised version was published online in July 2006 with corrections to the Cover Date.     

Spatial interactions in simple and combined-feature visual search.

To isolate the mechanisms responsible for spatial interactions in visual search, we investigated the effects of inter-element distance and positional jittering in both simple (in/s) and combined-feature (inverted V in Vs) search tasks in which the observer had to find a target in a background of similar nontargets. Thresholds, defined as the stimulus duration for 75% correct, were measured for 'present' and 'absent' target conditions as a function of background numerosity (ranging from 4 to 64 background elements), independently for four inter-element distances and three positional jittering conditions. Results show: (1) both simple and combined-feature search involve a parallel, capacity limited process, (2) thresholds for parallel search of simple features are directly related to inter-element distance whereas this has little effect on thresholds in combined-feature search, and (3) positional jittering has a direct effect on thresholds in combined-feature search and an inverse effect in simple-feature search. These results indicate that two different mechanisms of spatial interactions are involved in parallel search. The activation of each of the two mechanisms depends on the stimulus used. In parallel search for simple and dissimilar features, the underlying mechanism is a short-range one, based on lateral inhibition, whereas the parallel search for combined and similar features is based on a nontarget grouping mechanism which relies on facilitatory interactions between regular elements.     

Tabu search model selection for SVM

A model selection method based on tabu search is proposed to build support vector machines (binary decision functions) of reduced complexity and efficient generalization. The aim is to build a fast and efficient support vector machines classifier. A criterion is defined to evaluate the decision function quality which blends recognition rate and the complexity of a binary decision functions together. The selection of the simplification level by vector quantization, of a feature subset and of support vector machines hyperparameters are performed by tabu search method to optimize the defined decision function quality criterion in order to find a good sub-optimal model on tractable times.     

Quantifying frequency dependence of auditory search

In the present study, we examined the frequency dependence of auditory search performance. Detection thresholds were measured for an 800-Hz target tone in a sequence of distractor tones (informational masking) as a function of frequency separation between the target and the distractor tones. The results showed that the thresholds decreased monotonically with frequency separation increasing. To further quantify the frequency dependence of auditory search performance, we applied a roex function (Patterson and Moore, 1986) to estimate a filter bandwidth for the threshold data. The estimated bandwidth was wider than that of an auditory filter by a factor of five (Leek et al., 1991). This result, together with some earlier results (Mori, 2003), demonstrates the effectiveness of the informational masking we used.     

毛乌素沙地区域尺度生物结皮有机碳

生物结皮在旱区荒漠养分循环和碳氮固存等生态系统功能方面发挥着重要作用,尤其能通过光合作用固定CO₂,从而提高土壤有机碳含量。目前有关区域尺度生物结皮土壤有机碳认知的缺乏在一定程度上制约了土壤碳库的精准预测。本研究选取毛乌素沙地全域(4.22万km²)内45个样地,测算了藓结皮和藻结皮两类典型生物结皮及其下土壤的有机碳含量(SOC)和密度(SOCD),并结合气候、土壤和植被等指标,深入探讨了区域尺度下生物结皮有机碳的空间分布特征及其主控因素。结果表明: 1)与裸沙相比,生物结皮显著提升了土壤有机碳含量和密度,且藓结皮及其下土壤有机碳含量(4.93 g·kg^-1)和密度(0.41 kg·m^-2)均高于藻结皮(1.89 g·kg^-1、0.18 kg·m^-2)。2)区域尺度上,生物结皮的有机碳含量和密度具有明显的空间分布特征,呈现出由东北-中部、西部-东南方向递减的带状分布与块状镶嵌分布。3)生物结皮及其下土壤有机碳含量和密度主要受气候、土壤和植被的综合影响,并因生物结皮类型而异,藓结皮主要受年均最高温和蒸散力的影响,而藻结皮主要受水蒸气分压的影响。     

Putative role for a myosin motor in store-operated calcium entry

Store-operated calcium (SOC) entry is the most prominent mode of calcium entry in nonexcitable cells, although important questions remain regarding its mechanism(s) of activation and the molecular identity of SOC entry channels. Recent work using Drosophila melanogaster and mammalian cells suggest that myosin may play a central role in regulation of the open state of SOC entry channels. The most direct evidence for such a role for myosin motor function is in the Drosophila rhabdomere, where a myosin homolog appears to terminate channel signaling. Studies directly examining the contribution of myosin to mammalian SOC entry are lacking. However, several indirect lines of evidence support a role for myosin motor function in the control of calcium entry. Both inhibition of myosin light-chain kinase (the kinase responsible for myosin activation) and disruption of filamentous actin (the track for actomyosin motor function) reduces SOC entry and appear to prevent activation of a calcium-selective SOC entry current. Thus this review summarizes data—emphasizing recent evidence in mammalian systems—implicating myosin motor function in the control of SOC entry.     

Visual search in peripheral vision: learning effects and set-size dependence.

Feature search for a light bar with one orientation (or color) embedded in an array of bars with a very different orientation (or color) is quick, easy and independent of the number of array elements. In contrast, search for a conjunction target has a linear response time dependence on the number of distractors. Training can improve performance of both these tasks. We report that these properties may not be valid for eccentric stimulus presentation. In general, the two hemifields are not equally suited to search, and training is most effective in the weaker hemifield. In addition, the feature-search independence of set-size may not always be valid for stimulus arrays that are presented peripherally. Subjects were tested on orientation and color feature tasks, and on orientation-color conjunction search with 3 array sizes presented at fixation or eccentrically in the right or left hemifield. During a second testing session, improvement was so much greater for the non-preferred hemifield that sometimes the preference was switched. Surprisingly, preferred hemifield performance actually declined for some subjects. Thus, the hemifield preference effect seems related to competition, and perhaps an automatic attention-directing mechanism. We confirmed the central presentation set-size independence for feature search but found a great difference between large and small arrays when presentation was lateral. There are two sources of this array size effect: 1. Target eccentricity, demonstrated by comparing performance for different target locations with the same array size. 2. Target location uncertainty, seen by comparing performance for different size arrays when the target elements appeared at the same locations. Training also affected the array-size dependence, changing search performance from set-size dependent to independent or vice versa at the point of greatest training effect.     

Sequential search and the influence of male quality on female mating decisions

 The patterns of phenotypic association between mated males and females depend on the decision rules that individuals employ during search for a mate. We generalize the sequential search rule and examine how the shape of the function that relates a male character to the benefit of a mating decision influences the threshold value of the male trait that induces females to terminate search. If the fitness function is linear the optimal threshold value of a male character increases with the slope of the function. The phenotypic threshold criterion declines, all else being equal, if the fitness function is made more concave (or less convex) by an increase of the risk of the function. The expression of the trait in females has no effect on the optimal threshold value of a male character if the fitness function is linear and phenotypic values combine additively to influence the benefit of a mating decision; the phenotypic threshold criterion is ubiquitous among females. A convex fitness function induces females with high trait values to adopt a relatively high phenotypic threshold criterion, whereas a concave fitness function induces such females to adopt a low threshold value for the male trait. Thus, linear, convex and concave fitness functions effect random, assortative and disassortative combinations of phenotypes among mated individuals, respectively. Changes of female search behavior induced by changes of the distribution of a male character similarly depend on the shape of the fitness function. A variance-preserving increase of male trait values produces a relatively small increase of the threshold criterion for the male character if the fitness function is concave, relative to conditions in which the fitness function is either linear or convex. Our results suggest that a sequential search rule can in principle induce the kinds of mating patterns observed in nature and that the phenotypic association between mated individuals is likely to depend on how a male character translates into fitness, the distribution of the trait among males and attributes of searching females. Received: 20 September 1997 / Revised version: 13 August 1998     

新疆焉耆盆地绿洲区农田土壤有机碳储量动态模拟

以焉耆盆地绿洲区丝路重镇——焉耆回族自治县长期定位监测的数据为基础,实地采集800个土样进行土壤有机碳(SOC)实验室测试,进行点位模拟校验模型,并拓展到区域模拟,采用BCCC-CSM1.1气候模式,研究农田土壤有机碳密度分布特征及有机碳储量空间分布格局,为气候变化条件下,绿洲区耕地SOC储量和SOC密度变化提供数据支持。结果表明:(1) DNDC模型能够较好地模拟研究区农田的SOC及其动态变化,相关系数大于0.96,模拟值与观测值的均方根误差(RMSE)在0.48%—13.08%之间,模拟值与实测值显著相关。(2)点位模拟不同处理间SOC变化显示,不同土壤质地土壤有机碳含量差异明显,5年来SOC增长趋势表现为粉砂质壤土壤土砂质壤土。(3) 2017年焉耆县农田表层土壤有机碳总储量为0.44 Tg C,在未来30年里,在相应农业措施下,研究区农田0—20 cm土层SOC密度和储量呈显著增加趋势,单位面积碳增量增幅为-7%—29%;新增固碳量3.708×10~8—1.978×10~9 t,增幅为-5%—48%,呈现出"碳汇"趋势,这对恢复农田SOC的平衡和绿洲农业的可持续发展至关重要。     

RAG-3D: a search tool for RNA 3D substructures

To address many challenges in RNA structure/function prediction, the characterization of RNA''s modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.     

Associative search network: A reinforcement learning associative memory

An associative memory system is presented which does not require a teacher to provide the desired associations. For each input key it conducts a search for the output pattern which optimizes an external payoff or reinforcement signal. The associative search network (ASN) combines pattern recognition and function optimization capabilities in a simple and effective way. We define the associative search problem, discuss conditions under which the associative search network is capable of solving it, and present results from computer simulations. The synthesis of sensory-motor control surfaces is discussed as an example of the associative search problem.     

Optimization of brownian search strategies

What are the simplest search strategies that lead an animal to a particular target, what are their limitations, and what changes can be made to develop more effective strategies? To answer these question a class of search strategies was examined that require an animal to have only a minimal capacity for spatial orientation; the effectiveness of such strategies in solving the following basic search problem was determined. The animal begins its search at a distance r _o (starting distance) from a spatially fixed target. It detects the target when it has approached it to within a certain distance a (the detection radius). The analysed class of search strategies has the following characteristics: C1. The animal uses the same search strategy in all regions it enters. Therefore it needs no information as to the actual location of the target. C2. Its search strategy is constant in time. The animal has only to detect whether it has reached the target or not. C3. Once the animal has chosen a direction, it continues in that direction for a certain distance. This is the only way in which the preceding parts of the search affect the animal's decision as to the direction in which it will search next. In the long term the animal's movement directions are independent, with no preference for any particular direction. Despite their extreme simplicity in application these “Brownian” search strategies are remarkably successful (Fig. 1). Indeed, if the search is continued long enough the target is certain to be found. The success of the search depends in part on the search duration (Fig. 2) or the search-path length S, the starting distance and the detection radius. On the other hand, an animal can have a decisive influence on its degree of success simply by adjusting the frequency with which it changes its walking direction to match its sensory abilities. That is, a not-too-short Brownian search (S?r _o) is most successful when the searching animal, between the points at which it changes direction, walks approximately straight for a distance equal to the detection radius (Figs. 3 and 4). A further increase in search effectiveness is possible only by turning to another class of search strategies. These, however, demand that the animal either have more information about the position of its target at the beginning of the search or be able to organize its search behavior even over fairly long periods of time.     

Evolutionary optimization in multimodal search space

Optimization by a simple evolution strategy based on a mutation and selection scheme without recombination was tested for its efficiency in multimodal search space. A modified Rastrigin function served as an objective function providing fitness landscapes with many local optima. It turned out that the evolutionary algorithm including adaptive stepsize control is wellsuited for optimization. The process is able to efficiently surmount local energy barriers and converge to the global optimum. The relation between the optimization time available and the optimal number of offspring was investigated and a simple rule proposed. Several numbers of offspring are nearly equally suited in a smooth search space, whereas in rough fitness landscapes an optimum is observed. In either case both very large and very small numbers of offspring turned out to be unfavourable for optimization.     

Using search engine technology for protein function prediction

Prediction of protein function is one of the most challenging problems in the post-genomic era. In this paper, we propose a novel algorithm Improved ProteinRank (IPR) for protein function prediction, which is based on the search engine technology and the preferential attachment criteria. In addition, an improved algorithm IPRW is developed from IPR to be used in the weighted protein?protein interaction (PPI) network. The proposed algorithms IPR and IPRW are applied to the PPI network of S.cerevisiae. The experimental results show that both IPR and IPRW outweigh the previous methods for the prediction of protein functions.     

Medline search engine for finding genetic markers with biological significance

MOTIVATION: Genome-wide high density SNP association studies are expected to identify various SNP alleles associated with different complex disorders. Understanding the biological significance of these SNP alleles in the context of existing literature is a major challenge since existing search engines are not designed to search literature for SNPs or other genetic markers. The literature mining of gene and protein functions has received significant attention and effort while similar work on genetic markers and their related diseases is still in its infancy. Our goal is to develop a web-based tool that facilitates the mining of Medline literature related to genetic studies and gene/protein function studies. Our solution consists of four main function modules for (1) identification of different types of genetic markers or genetic variations in Medline records (2) distinguishing positive versus negative linkage or association between genetic markers and diseases (3) integrating marker genomic location data from different databases to enable the retrieval of Medline records related to markers in the same linkage disequilibrium region (4) and a web interface called MarkerInfoFinder to search, display, sort and download Medline citation results. Tests using published data suggest MarkerInfoFinder can significantly increase the efficiency of finding genetic disorders and their underlying molecular mechanisms. The functions we developed will also be used to build a knowledge base for genetic markers and diseases. AVAILABILITY: The MarkerInfoFinder is publicly available at: http://brainarray.mbni.med.umich.edu/brainarray/datamining/MarkerInfoFinder.     

Metagenomic and 14C tracing evidence for autotrophic microbial CO2 fixation in paddy soils

Autotrophic carbon dioxide (CO₂) fixation by microbes is ubiquitous in the environment and potentially contributes to the soil organic carbon (SOC) pool. However, the multiple autotrophic pathways of microbial carbon assimilation and fixation in paddy soils remain poorly characterized. In this study, we combine metagenomic analysis with ¹⁴C-labelling to investigate all known autotrophic pathways and CO₂ assimilation mechanisms in five typical paddy soils from southern China. Marker genes of six autotrophic pathways are detected in all soil samples, which are dominated by the cbbL genes (67%–82%) coding the ribulose-bisphosphate carboxylase large chain in the Calvin cycle. These marker genes are associated with a broad range of phototrophic and chemotrophic genera. Significant amounts of ¹⁴C-CO₂ are assimilated into SOC (74.3–175.8 mg ¹⁴C kg⁻¹) and microbial biomass (5.2–24.1 mg ¹⁴C kg⁻¹) after 45 days incubation, where more than 70% of ¹⁴C-SOC was concentrated in the relatively stable humin fractions. These results show that paddy soil microbes contain the genetic potential for autotrophic carbon fixation spreading over broad taxonomic ranges, and can incorporate atmospheric carbon into organic components, which ultimately contribute to the stable SOC pool.