TPX: Biomedical literature search made easy

TPX is a web-based PubMed search enhancement tool that enables faster article searching using analysis and exploration features. These features include identification of relevant biomedical concepts from search results with linkouts to source databases, concept based article categorization, concept assisted search and filtering, query refinement. A distinguishing feature here is the ability to add user-defined concept names and/or concept types for named entity recognition. The tool allows contextual exploration of knowledge sources by providing concept association maps derived from the MEDLINE repository. It also has a full-text search mode that can be configured on request to access local text repositories, incorporating entity co-occurrence search at sentence/paragraph levels. Local text files can also be analyzed on-the-fly. Availability: http://tpx.atc.tcs.com     

Saltatory search in a lateral line predator

The dwarf scorpionfish Scorpaena papillosa detected the hydrodynamic signals produced by prey with the mechanosensory lateral line. This species displayed a pause and move search pattern that is consistent with a saltatory search. The pause phase of the search cycle was probably used to detect prey because pauses often ended early in order to initiate an approach at prey and prey were detected throughout the search space. The move phase of the search cycle repositioned the fish so that it moved approximately a third of the reactive distance. Move distance was found to be the most important factor in gaining novel search space. Turning was shown to be relatively unimportant in gaining novel search space with a high frequency of low turn angles made by the fish. The dwarf scorpionfish, however, exhibited a spiralling or looping pattern over a search path exhibiting a turn bias towards either the left or right. The dwarf scorpionfish adopted a search behaviour that is consistent with a saltatory search and efficient for lateral line predation.     

Saltatory search: a theoretical analysis

Many animal search in a saltatory fashion: they move forward,pause briefly, and move forward again. Although many optimal-foragingmodels have been developed, most do not address how an animalsearches for food. We view search strategies as "time-distance"functions to allow not only for the possibility of oscillationsin body speed, as implied by saltatory search, but other movementpatterns as well, including cruise search. The key feature ofour models is distinguishing between the body position and thescan position (where the forager is looking). We see the varyingmovement of saltatory search as a consequence of the curvaturein the functions that relate body speed to benefits (Jensen'sinequality)     

Ant search behaviour analysis with a video frame grabber

Summary Frame grabbers are video digitizers that allow a high-speed capture and manipulation of video images. In this paper we discuss the use of frame grabbers to achieve real-time or videotape automatic tracking of a moving insect (an ant). We describe the basic equipment required to use this technology and explain the steps involved in the tracking procedure. The potential applications of this technique in the study of search behaviour in flightless social insect species such as ants and termites are discussed.     

Mate choice and optimal search behavior: Fitness returns under the fixed sample and sequential search strategies

The behavior of a female in search of a mate determines the likelihood that she encounters a high-quality male in the search process. The fixed sample (best-of-n) search strategy and the sequential search (fixed threshold) strategy are two prominent models of search behavior. The sequential search strategy dominates the former strategy—yields an equal or higher expected net fitness return to searchers—when search costs are nontrivial and the distribution of quality among prospective mates is uniform or truncated normal. In this paper our objective is to determine whether there are any search costs or distributions of male quality for which the sequential search strategy is inferior to the fixed sample search strategy. The two search strategies are derived under general conditions in which females evaluate encountered males by inspection of an indicator character that has some functional relationship to male quality. The solutions are identical to the original models when the inspected male attribute is itself male quality. The sequential search strategy is shown to dominate the fixed sample search strategy for all search costs and distributions of male quality. Low search costs have been implicated to explain empirical observations that are consistent with the use of a fixed sample search strategy, but under conditions in which the original models were derived there is no search cost or distribution of male quality that favors the fixed sample search strategy. Plausible alternative explanations for the apparent use of this search strategy are discussed.     

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.     

Modelling eye movements in a categorical search task

We introduce a model of eye movements during categorical search, the task of finding and recognizing categorically defined targets. It extends a previous model of eye movements during search (target acquisition model, TAM) by using distances from an support vector machine classification boundary to create probability maps indicating pixel-by-pixel evidence for the target category in search images. Other additions include functionality enabling target-absent searches, and a fixation-based blurring of the search images now based on a mapping between visual and collicular space. We tested this model on images from a previously conducted variable set-size (6/13/20) present/absent search experiment where participants searched for categorically defined teddy bear targets among random category distractors. The model not only captured target-present/absent set-size effects, but also accurately predicted for all conditions the numbers of fixations made prior to search judgements. It also predicted the percentages of first eye movements during search landing on targets, a conservative measure of search guidance. Effects of set size on false negative and false positive errors were also captured, but error rates in general were overestimated. We conclude that visual features discriminating a target category from non-targets can be learned and used to guide eye movements during categorical search.     

Fast tree search for a triangular lattice model of protein folding

Using a triangular lattice model to study the designability of protein folding, we overcame the parity problem of previous cubic lattice model and enumerated all the sequences and compact structures on a simple two-dimensional triangular lattice model of size 4 5 6 5 4. We used two types of amino acids, hydrophobic and polar, to make up the sequences, and achieved 223W212 different sequences excluding the reverse symmetry sequences. The total string number of distinct compact structures was 219,093, excluding reflection symmetry in the self-avoiding path of length 24 triangular lattice model. Based on this model, we applied a fast search algorithm by constructing a cluster tree. The algorithm decreased the computation by computing the objective energy of non-leaf nodes. The parallel experiments proved that the fast tree search algorithm yielded an exponential speed-up in the model of size 4 5 6 5 4. Designability analysis was performed to understand the search result.     

Cuckoo search epistasis: a new method for exploring significant genetic interactions

The advent of high-throughput sequencing technology has resulted in the ability to measure millions of single-nucleotide polymorphisms (SNPs) from thousands of individuals. Although these high-dimensional data have paved the way for better understanding of the genetic architecture of common diseases, they have also given rise to challenges in developing computational methods for learning epistatic relationships among genetic markers. We propose a new method, named cuckoo search epistasis (CSE) for identifying significant epistatic interactions in population-based association studies with a case–control design. This method combines a computationally efficient Bayesian scoring function with an evolutionary-based heuristic search algorithm, and can be efficiently applied to high-dimensional genome-wide SNP data. The experimental results from synthetic data sets show that CSE outperforms existing methods including multifactorial dimensionality reduction and Bayesian epistasis association mapping. In addition, on a real genome-wide data set related to Alzheimer''s disease, CSE identified SNPs that are consistent with previously reported results, and show the utility of CSE for application to genome-wide data.     

Detecting meaning in dream reports: An extension of a word search approach.

Building on previous investigations of waking–dreaming continuities using word search technology (Bulkeley 2009a, 2009b; Domhoff & Schneider, 2008), we demonstrate that a blind analysis of a dream series using only word search methods can accurately predict many important aspects of the individual's waking life, including personality attributes, relationships, activities, and cultural preferences. Results from a study of the “Van” dream series (N = 192) show that blind inferences drawn from a word search analysis were almost entirely accurate according to the dreamer. After presenting these findings we discuss several remaining shortcomings and suggest ways of improving the method for use by other researchers involved in the search for a more systematic understanding of meaning in dreams. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling

Recently, a series of closely related theoretical constructs termed the "topomer search model" (TSM) has been proposed for the folding mechanism of small, single-domain proteins. A basic assumption of the proposed scenarios is that the rate-limiting step in folding is an essentially unbiased, diffusive search for a conformational state called the native topomer defined by an overall native-like topological pattern. Successes in correlating TSM-predicted folding rates with that of real proteins have been interpreted as experimental support for the model. To better delineate the physics entailed, key TSM concepts are examined here using extensive Langevin dynamics simulations of continuum C(alpha) chain models. The theoretical native topomers of four experimentally well-studied two-state proteins are characterized. Consistent with the TSM perspective, we found that the sizes of the native topomers increase with experimental folding rate. However, a careful determination of the corresponding probabilities that the native topomers are populated during a random search fails to reproduce the previously predicted folding rates. Instead, our results indicate that an unbiased TSM search for the native topomer amounts to a Levinthal-like process that would take an impossibly long average time to complete. Furthermore, intraprotein contacts in all four native topomers considered exhibit no apparent correlation with the experimental phi-values determined from the folding kinetics of these proteins. Thus, the present findings suggest that certain basic, generic yet essential energetic features in protein folding are not accounted for by TSM scenarios to date.     

Adaptive search in juvenile plaice foraging for aggregated and dispersed prey

Juvenile plaice Pleuronectes platessa in a laboratory arena used intensive search behaviour, characterized by short movements and frequent turning, in the five movements before and after attacking a prey in an aggregated distribution. They used extensive search behaviour with, on average, longer movements and less turning at all other times. Intensive search was, apparently, triggered by a high local density of prey but not by isolated prey. This response to local prey density resulted in area-restricted search when prey were aggregated and win-shift behaviour when prey were dispersed. There was no evidence that the use of intensive search increased with experience of aggregated prey. It therefore appears that the fish were able to exploit encountered prey distribution patterns using their immediate perceptions rather than prior experience.     

Evidence of a rheotactic component in the odour search behaviour of freshwater eels

The detection of food odour by the freshwater eels, Anguilla australis and Anguilla dieffenbachii released a behavioural response to flow that resulted in direct upstream movement toward the odour source. Changes in various orientation parameters were observed as eels neared the source. Eels had substantially lower swimming velocities and considerably more variable heading and course angles close to the odour source (≤0·9 m) than further away (>0·9 m). Observed changes in orientation parameters were primarily due to changes in the behaviour of a searcher following odour loss. Cross-stream movements were initiated when the eel moved beyond the lateral margins of the odour plume. The behavioural switch from odour-conditioned rheotaxis to cross-stream casting following odour loss occurred more frequently close to the odour source where the plume was most narrow. Odour-conditioned rheotaxis enables the searcher to move quickly and efficiently toward the odour source without the need to extract directional information from a highly intermittent and complex chemical signal.     

鸡dbSNP数据库的检索与应用

dbSNP数据库为广大研究者提供了丰富的SNPs信息,充分地利用dbSNP数据库中的资源将大幅度降低研究成本提高研究效率。结合本实验室的研究工作,对鸡dbSNP数据库的检索和应用进行了一些探索。认为根据研究目的的不同,dbSNP数据库的检索和应用有必要同其它的数据库相结合。     

Increased turning per unit distance as an area-restricted search mechanism in a pause-travel predator, juvenile plaice, foraging for buried bivalves

During searching, discovery of a prey patch by juvenile plaice Pleuronectes platessa was associated with a change from extensive to intensive search behaviour several moves before an attack on a prey. Intensive search behaviour was characterized by reduced distance of moves, a greater rate of turning per unit distance and shorter pauses between moves. The increase in turn rate was associated with area-restricted seaching, while a decrease in distances moved suggests that plaice search more efficiently for prey when stationary than while moving. The klinokinetic mechanism that appears to regulate search behaviour in juvenile plaice should allow efficient exploitation of a range of prey distribution patterns based on localized cues alone. Such a mechanism is especially useful to a migratory predator, like plaice, whose foraging is subject to time constraints imposed by tidally available feeding areas.     

Optimum search speed and activity: a dynamic game in a three-link trophic system

We analysed how a consumer should simultaneously trade-off search speed and time active in a game with predators that optimise their search speed. Both the consumers and the predators are continuously reproducing and maximise fitness by maximising the per capita growth rate. The impact of the predator's presence on consumer behaviour, and the effects of type I and II functional responses on the behaviour of both species are considered. In the analyses, consumers were allowed to co-ordinate activity or behave independently in relation to other consumers. The ESS-analysis of the game ensures that no mutant can invade the system. The independent activity was found to be optimal in all analyses, while the co-ordinated activity was only optimal at full activity where the two activity strategies coincided. The model showed that consumers should change activity to account for predation risk. Activity generally decreased with predation risk. Concerning the energetic aspects, both activity and search speed were important to account for the reproductive output. The functional responses influenced the optimum activity and search speed of consumers and predators. In general, the optimum behaviours showed complex non-linear responses in relation to the resource and the consumer density. A predator type II functional response had profound impacts on the properties of the optima, the stability and presence of alternative strategies. As a result of the optimum behaviours, the realised functional responses of both species became sigmoidal.     

Sources of information controlling motor patterns in arthropod local search orientation

Search orientation is controlled by information that is stored genetically, idiothetically or through learning and that is gained from internal and external sensory systems. Sources of variation in motor patterns could derive from any of the types of information, or could originate during the execution of the instructions derived from orientation information. Local search after resource utilization in the flies Musca demestica and Drosophila melanogaster can be addressed as an initial increase in turning rate and decrease in locomotory rate, followed by a transition in both measures to a lower turning rate and a higher locomotory rate characteristic of ranging. The search tactic of flies promotes accrual of discrete resources in a patch. A forward-moving tendency, combined with a “noisy” looping motor pattern, enhances resource-finding in both linear and non-linear resource patterns. The period before a fly leaves a patch—its giving-up-time—is a function of current resource density and the slope of the transition from local search to ranging: once a fly switches to the relatively straight path characteristic of ranging, the chances of it leaving the patch depends on whether or not another resource is encountered. Duration of local search is dependent on the genotype of an individual, level of starvation or satiation, resource quality (sucrose concentration) and quantity (patch size) and presence of resource-specific sensory information.