Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Guided search for triple conjunctions.

ABSTRACT: A key tenet of feature integration theory and of related theories such as guided search (GS) is that the binding of basic features requires attention. This would seem to predict that conjunctions of features of objects that have not been attended should not influence search. However, Found (1998) reported that an irrelevant feature (size) improved the efficiency of search for a Color × Orientation conjunction if it was correlated with the other two features across the display, as compared to the case in which size was not correlated with color and orientation features. We examined this issue with somewhat different stimuli. We used triple conjunctions of color, orientation, and shape (e.g., search for a red, vertical, oval-shaped item). This allowed us to manipulate the number of features that each distractor shared with the target (sharing) and it allowed us to vary the total number of distractor types (and, thus, the number of groups of identical items: grouping). We found that these triple conjunction searches were generally very efficient--producing very shallow Reaction Time × Set Size slopes, consistent with strong guidance by basic features. Nevertheless, both of the variables, sharing and grouping, modulated performance. These influences were not predicted by previous accounts of GS; however, both can be accommodated in a GS framework. Alternatively, it is possible, though not necessary, to see these effects as evidence for "preattentive binding" of conjunctions.

SUBMITTER: Nordfang M

PROVIDER: S-EPMC5565881 | biostudies-other | 2014 Aug

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Vestibular-guided visual search.

Project description:The amnesic symptoms that accompany vestibular dysfunction point to a functional relationship between the vestibular and visual memory systems. However, little is known about the underpinning cognitive processes. As a starting point, we sought evidence for a type of cross-modal interaction commonly observed between other sensory modalities in which the identification of a target (in this case, visual) is facilitated if earlier coupled to a unique, temporally coincident stimulus from another sensory domain (in this case, vestibular). Participants first performed a visual detection task in which stimuli appeared at random locations within a computerised grid. Unknown to participants, the onset of one particular stimulus was accompanied by a brief, sub-sensory pulse of galvanic vestibular stimulation (GVS). Across two visual search experiments, both old and new targets were identified faster when presented in the grid location at which the GVS-paired visual stimulus had appeared in the earlier detection task. This location advantage appeared to be based on relative rather than absolute spatial co-ordinates since the effect held when the search grid was rotated 90°. Together these findings indicate that when individuals return to a familiar visual scene (here, a 2D grid), visual judgements are facilitated when targets appear at a location previously associated with a unique, task-irrelevant vestibular cue. This novel case of multisensory interplay has broader implications for understanding how vestibular signals inform cognitive processes and helps constrain the growing therapeutic application of GVS.

| S-EPMC7080682 | biostudies-literature

Multistep retrosynthesis combining a disconnection aware triple transformer loop with a route penalty score guided tree search.

Project description:Computer-aided synthesis planning (CASP) aims to automatically learn organic reactivity from literature and perform retrosynthesis of unseen molecules. CASP systems must learn reactions sufficiently precisely to propose realistic disconnections, while avoiding overfitting to leave room for diverse options, and explore possible routes such as to allow short synthetic sequences to emerge. Herein we report an open-source CASP tool proposing original solutions to both challenges. First, we use a triple transformer loop (TTL) predicting starting materials (T1), reagents (T2), and products (T3) to explore various disconnection sites defined by combining systematic, template-based, and transformer-based tagging procedures. Second, we integrate TTL into a multistep tree search algorithm (TTLA) prioritizing sequences using a route penalty score (RPScore) considering the number of steps, their confidence score, and the simplicity of all intermediates along the route. Our approach favours short synthetic routes to commercial starting materials, as exemplified by retrosynthetic analyses of recently approved drugs.

| S-EPMC10510629 | biostudies-literature

SHAPE-guided RNA structure homology search and motif discovery

Project description:The rapidly growing popularity of RNA structure probing methods is leading to increasingly large amounts of available RNA structure information. This demands the development of efficient tools for the identification of RNAs sharing regions of structural similarity by direct comparison of their reactivity profiles, hence enabling the discovery of conserved structural features. We here introduce SHAPEwarp, a largely sequence-agnostic SHAPE-guided algorithm for the identification of structurally-similar regions in RNA molecules. Analysis of Dengue, Zika and coronavirus genomes recapitulates known regulatory RNA structures and identifies novel highly-conserved structural elements. This work represents a preliminary step towards the model-free search and identification of shared RNA structural features within transcriptomes.

2022-03-04 | GSE189259 | GEO

Guided nuclear exploration increases CTCF target search efficiency.

Project description:The enormous size of mammalian genomes means that for a DNA-binding protein the number of nonspecific, off-target sites vastly exceeds the number of specific, cognate sites. How mammalian DNA-binding proteins overcome this challenge to efficiently locate their target sites is not known. Here, through live-cell single-molecule tracking, we show that CCCTC-binding factor, CTCF, is repeatedly trapped in small zones that likely correspond to CTCF clusters, in a manner that is largely dependent on an internal RNA-binding region (RBRi). We develop a new theoretical model called anisotropic diffusion through transient trapping in zones to explain CTCF dynamics. Functionally, transient RBRi-mediated trapping increases the efficiency of CTCF target search by ~2.5-fold. Overall, our results suggest a 'guided' mechanism where CTCF clusters concentrate diffusing CTCF proteins near cognate binding sites, thus increasing the local ON-rate. We suggest that local guiding may allow DNA-binding proteins to more efficiently locate their target sites.

| S-EPMC7036004 | biostudies-literature

Categorical grouping is not required for guided conjunction search.

Project description:Knowledge of target features can guide attention in many conjunction searches in a top-down manner. For example, in search of a red vertical line among blue vertical and red horizontal lines, observers can guide attention toward all red items and all vertical items. In typical conjunction searches, distractors often form perceptually vivid, categorical groups of identical objects. This could favor the efficient search via guidance of attention to these "segmentable" groups. Can attention be guided if the distractors are not neatly segmentable (e.g., if colors vary continuously from red through purple to blue)? We tested search for conjunctions of color × orientation (Experiments 1, 3, 4, 5) or length × orientation (Experiment 2). In segmentable conditions, distractors could form two clear groups (e.g., blue steep and red flat). In non-segmentable conditions, distractors varied smoothly from red to blue and/or steep to flat; thus, discouraging grouping and increasing overall heterogeneity. We found that the efficiency of conjunction search was reasonably high and unaffected by segmentability. The same lack of segmentability had a detrimental effect on feature search (Experiment 4) and on conjunction search, if target information was limited to one feature (e.g., find the odd item in the red set, "subset search," Experiment 3). Guidance in conjunction search may not require grouping and segmentation cues that are very important in other tasks like texture discrimination. Our results support an idea of simultaneous, parallel top-down guidance by multiple features and argue against models suggesting sequential guidance by each feature in turn.

| S-EPMC7463200 | biostudies-literature

Network-guided search for genetic heterogeneity between gene pairs.

Project description:MotivationCorrelating genetic loci with a disease phenotype is a common approach to improve our understanding of the genetics underlying complex diseases. Standard analyses mostly ignore two aspects, namely genetic heterogeneity and interactions between loci. Genetic heterogeneity, the phenomenon that genetic variants at different loci lead to the same phenotype, promises to increase statistical power by aggregating low-signal variants. Incorporating interactions between loci results in a computational and statistical bottleneck due to the vast amount of candidate interactions.ResultsWe propose a novel method SiNIMin that addresses these two aspects by finding pairs of interacting genes that are, upon combination, associated with a phenotype of interest under a model of genetic heterogeneity. We guide the interaction search using biological prior knowledge in the form of protein-protein interaction networks. Our method controls type I error and outperforms state-of-the-art methods with respect to statistical power. Additionally, we find novel associations for multiple Arabidopsis thaliana phenotypes, and, with an adapted variant of SiNIMin, for a study of rare variants in migraine patients.Availability and implementationCode available at https://github.com/BorgwardtLab/SiNIMin.Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC8034561 | biostudies-literature

Sniff-synchronized, gradient-guided olfactory search by freely moving mice.

Project description:For many organisms, searching for relevant targets such as food or mates entails active, strategic sampling of the environment. Finding odorous targets may be the most ancient search problem that motile organisms evolved to solve. While chemosensory navigation has been well characterized in microorganisms and invertebrates, spatial olfaction in vertebrates is poorly understood. We have established an olfactory search assay in which freely moving mice navigate noisy concentration gradients of airborne odor. Mice solve this task using concentration gradient cues and do not require stereo olfaction for performance. During task performance, respiration and nose movement are synchronized with tens of milliseconds precision. This synchrony is present during trials and largely absent during inter-trial intervals, suggesting that sniff-synchronized nose movement is a strategic behavioral state rather than simply a constant accompaniment to fast breathing. To reveal the spatiotemporal structure of these active sensing movements, we used machine learning methods to parse motion trajectories into elementary movement motifs. Motifs fall into two clusters, which correspond to investigation and approach states. Investigation motifs lock precisely to sniffing, such that the individual motifs preferentially occur at specific phases of the sniff cycle. The allocentric structure of investigation and approach indicates an advantage to sampling both sides of the sharpest part of the odor gradient, consistent with a serial-sniff strategy for gradient sensing. This work clarifies sensorimotor strategies for mouse olfactory search and guides ongoing work into the underlying neural mechanisms.

| S-EPMC8169121 | biostudies-literature

Potent antibiotic design via guided search from antibacterial activity evaluations.

Project description:MotivationThe emergence of drug-resistant bacteria makes the discovery of new antibiotics an urgent issue, but finding new molecules with the desired antibacterial activity is an extremely difficult task. To address this challenge, we established a framework, MDAGS (Molecular Design via Attribute-Guided Search), to optimize and generate potent antibiotic molecules.ResultsBy designing the antibacterial activity latent space and guiding the optimization of functional compounds based on this space, the model MDAGS can generate novel compounds with desirable antibacterial activity without the need for extensive expensive and time-consuming evaluations. Compared with existing antibiotics, candidate antibacterial compounds generated by MDAGS always possessed significantly better antibacterial activity and ensured high similarity. Furthermore, although without explicit constraints on similarity to known antibiotics, these candidate antibacterial compounds all exhibited the highest structural similarity to antibiotics of expected function in the DrugBank database query. Overall, our approach provides a viable solution to the problem of bacterial drug resistance.Availability and implementationCode of the model and datasets can be downloaded from GitHub (https://github.com/LiangYu-Xidian/MDAGS).Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC9897189 | biostudies-literature

SHAPE-guided RNA structure homology search and motif discovery

Project description:SHAPE-guided RNA structure homology search and motif discovery

| PRJNA782295 | ENA

Endoscopic ultrasound-guided radiofrequency ablation in gastroenterology: New horizons in search.

Project description:Radiofrequency ablation (RFA) has been widely used for the treatment of various solid organ malignancies. Over the last decade, endosonographers have gradually shifted the application of RFA from porcine models to humans to treat a spectrum of diseases. RFA is performed in patients with pancreatic carcinoma who are not candidates for surgery. In this paper, we will discuss various indications for RFA, its procedural details and complications. At present, endoscopic ultrasound-guided RFA is gradually incorporated into the management of various diseases and opens a new avenue for disease treatment.

| S-EPMC5526759 | biostudies-other

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data