Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks

In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.
Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from “seed” lists of human Entrez gene names. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list. Genes2Networks is available at http://actin.pharm.mssm.edu/genes2networks.
Genes2Network is a powerful web-based software application tool that can help experimental biologists to interpret high-throughput experimental results used in genomics and proteomics studies where the output of these experiments is a list of significantly changing genes or proteins. The system can be used to find relationships between nodes from the seed list, and predict novel nodes that play a key role in a common function

Resting‐state fMRI detects the effects of learning in short term: A visual search training study

Can resting-state functional connectivity (rs-FC) detect the impact of learning on the brain inthe short term? To test this possibility, we have combined task-FC and rs-FC tested before andafter a 30-min visual search training. Forty-two healthy adults (20 men) divided into no-contactcontrol and trained groups completed the study. We studied the connectivity between fourdifferent regions of the brain involved in visual search: the primary visual area, the right poste-rior parietal cortex (rPPC), the right dorsolateral prefrontal cortex (rDLPFC), and the dorsalanterior cingulate cortex (dACC). Task-FC showed increased connectivity between the rPPCand rDLPFC and between the dACC and rDLPFC from pretraining to posttraining for boththe control group and the trained group, suggesting that connectivity between these areasincreased with task repetition. In rs-FC, we found enhanced connectivity between theseregions in the trained group after training, especially in those with better learning. Whole brainindependent component analyses did not reveal any change in main networks after training.These results imply that rs-FC may not only predict individual differences in task performance,but rs-FC might also serve to monitor the impact of learning on the brain after short periodsof cognitive training, localizing them in brain areas specifically involved in training

Fixation instruction influences gaze cueing

Studies have shown that perceiving another person's gaze shift facilitates responses in the direction of the perceived gaze shift. While it is often assumed that participants in these experiments remain fixated on the cue in the cueing interval, eye gaze is not always recorded to confirm this. The data presented here suggest that the effect of gaze cues on responses to peripheral targets depends on whether participants make eye movements prior to the onset of the target. Participants who were required to fixate showed cueing effects at short cue-target intervals, but no cueing at later intervals. Participants who could look around, often chose to do so, and showed the same positive cueing effects at the shorter interval, but negative cueing effects (suggestive of inhibition of return) at the longer interval

Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases

<p>Abstract</p> <p>Background</p> <p>In recent years, mammalian protein-protein interaction network databases have been developed. The interactions in these databases are either extracted manually from low-throughput experimental biomedical research literature, extracted automatically from literature using techniques such as natural language processing (NLP), generated experimentally using high-throughput methods such as yeast-2-hybrid screens, or interactions are predicted using an assortment of computational approaches. Genes or proteins identified as significantly changing in proteomic experiments, or identified as susceptibility disease genes in genomic studies, can be placed in the context of protein interaction networks in order to assign these genes and proteins to pathways and protein complexes.</p> <p>Results</p> <p>Genes2Networks is a software system that integrates the content of ten mammalian interaction network datasets. Filtering techniques to prune low-confidence interactions were implemented. Genes2Networks is delivered as a web-based service using AJAX. The system can be used to extract relevant subnetworks created from "seed" lists of human Entrez gene symbols. The output includes a dynamic linkable three color web-based network map, with a statistical analysis report that identifies significant intermediate nodes used to connect the seed list.</p> <p>Conclusion</p> <p>Genes2Networks is powerful web-based software that can help experimental biologists to interpret lists of genes and proteins such as those commonly produced through genomic and proteomic experiments, as well as lists of genes and proteins associated with disease processes. This system can be used to find relationships between genes and proteins from seed lists, and predict additional genes or proteins that may play key roles in common pathways or protein complexes.</p

Inhibition of Return in the visual field

Inhibition of return (IOR) as an indicator of attentional control is characterized by an eccentricity effect, that is, the more peripheral visual field shows a stronger IOR magnitude relative to the perifoveal visual field. However, it could be argued that this eccentricity effect may not be an attention effect, but due to cortical magnification. To test this possibility, we examined this eccentricity effect in two conditions: the same-size condition in which identical stimuli were used at different eccentricities, and the size-scaling condition in which stimuli were scaled according to the cortical magnification factor (M-scaling), thus stimuli being larger at the more peripheral locations. The results showed that the magnitude of IOR was significantly stronger in the peripheral relative to the perifoveal visual field, and this eccentricity effect was independent of the manipulation of stimulus size (same-size or size-scaling). These results suggest a robust eccentricity effect of IOR which cannot be eliminated by M-scaling. Underlying neural mechanisms of the eccentricity effect of IOR are discussed with respect to both cortical and subcortical structures mediating attentional control in the perifoveal and peripheral visual field

Sex differences in eye gaze and symbolic cueing of attention

Observing a face with averted eyes results in a reflexive shift of attention to the gazed-at location. Here we present results that show that this effect is weaker in males than in females (Experiment 1). This result is predicted by the ‘extreme male brain’ theory of autism (Baron-Cohen, 2003), which suggests that males in the normal population should display more autism-like traits than females (e.g., poor joint attention). Indeed, participants′ scores on the Autism-Spectrum Quotient (Baron-Cohen, Wheelwright, Stott, Bolton, & Goodyear, 2001) negatively correlated with cueing magnitude. Furthermore, exogenous orienting did not differ between the sexes in two peripheral cueing experiments (Experiments 2a and 2b). However, a final experiment showed that using non-predictive arrows instead of eyes as a central cue also revealed a large gender difference. This demonstrates that reduced orienting from central cues in males generalizes beyond gaze cues. These results show that while peripheral cueing is equivalent in the male and female brains, the attention systems of the two sexes treat noninformative symbolic cues very differently

RAMP: a benchmark for evaluating robotic assembly manipulation and planning

We introduce RAMP, an open-source robotics benchmark inspired by real-world industrial assembly tasks. RAMP consists of beams that a robot must assemble into specified goal configurations using pegs as fasteners. As such, it assesses planning and execution capabilities, and poses challenges in perception, reasoning, manipulation, diagnostics, fault recovery, and goal parsing. RAMP has been designed to be accessible and extensible. Parts are either 3D printed or otherwise constructed from materials that are readily obtainable. The design of parts and detailed instructions are publicly available. In order to broaden community engagement, RAMP incorporates fixtures such as April Tags which enable researchers to focus on individual sub-tasks of the assembly challenge if desired. We provide a full digital twin as well as rudimentary baselines to enable rapid progress. Our vision is for RAMP to form the substrate for a community-driven endeavour that evolves as capability matures