The orienting mouse: An input device with attitude

This paper presents a modified computer mouse, the Orienting Mouse, which delivers orientation as an additional dimension of input; when the mouse is moved on a flat surface it reports, in addition to the conventional x, y translation, angular rotation of the device in the x, y plane. The orienting mouse preserves important properties of the standard mouse; all measurements are relative and movement is tracked only while the mouse is on its flat surface. If the user lets go of the mouse, leaving it on the surface, its position and orientation do not change until it is touched again. Picking the mouse up and putting it down in a different orientation leaves the angle and position unchanged. While the concept of sensing mouse rotation is not new, our work focuses on movement and navigation in 3D, rather than on precision positioning tasks. We describe a number of sample applications developed to test its effectiveness in this context. Specific features exploited and described include (i) an algorithm for calculating the mouse angle which cancels drift between the two sensors, and (ii) the use of angular gearing which avoids unnatural and uncomfortable hand positions when moving through large angles; informal user testing validates this idea

Impaired perceptual learning in a mouse model of Fragile X syndrome is mediated by parvalbumin neuron dysfunction and is reversible.

To uncover the circuit-level alterations that underlie atypical sensory processing associated with autism, we adopted a symptom-to-circuit approach in the Fmr1-knockout (Fmr1-/-) mouse model of Fragile X syndrome. Using a go/no-go task and in vivo two-photon calcium imaging, we find that impaired visual discrimination in Fmr1-/- mice correlates with marked deficits in orientation tuning of principal neurons and with a decrease in the activity of parvalbumin interneurons in primary visual cortex. Restoring visually evoked activity in parvalbumin cells in Fmr1-/- mice with a chemogenetic strategy using designer receptors exclusively activated by designer drugs was sufficient to rescue their behavioral performance. Strikingly, human subjects with Fragile X syndrome exhibit impairments in visual discrimination similar to those in Fmr1-/- mice. These results suggest that manipulating inhibition may help sensory processing in Fragile X syndrome

Biochemical pathways represented by Gene Ontology-Causal Activity Models identify distinct phenotypes resulting from mutations in pathways.

Gene inactivation can affect the process(es) in which that gene acts and causally downstream ones, yielding diverse mutant phenotypes. Identifying the genetic pathways resulting in a given phenotype helps us understand how individual genes interact in a functional network. Computable representations of biological pathways include detailed process descriptions in the Reactome Knowledgebase and causal activity flows between molecular functions in Gene Ontology-Causal Activity Models (GO-CAMs). A computational process has been developed to convert Reactome pathways to GO-CAMs. Laboratory mice are widely used models of normal and pathological human processes. We have converted human Reactome GO-CAMs to orthologous mouse GO-CAMs, as a resource to transfer pathway knowledge between humans and model organisms. These mouse GO-CAMs allowed us to define sets of genes that function in a causally connected way. To demonstrate that individual variant genes from connected pathways result in similar but distinguishable phenotypes, we used the genes in our pathway models to cross-query mouse phenotype annotations in the Mouse Genome Database (MGD). Using GO-CAM representations of 2 related but distinct pathways, gluconeogenesis and glycolysis, we show that individual causal paths in gene networks give rise to discrete phenotypic outcomes resulting from perturbations of glycolytic and gluconeogenic genes. The accurate and detailed descriptions of gene interactions recovered in this analysis of well-studied processes suggest that this strategy can be applied to less well-understood processes in less well-studied model systems to predict phenotypic outcomes of novel gene variants and to identify potential gene targets in altered processes

The mouse genome database (MGD): new features facilitating a model system

The mouse genome database (MGD, ), the international community database for mouse, provides access to extensive integrated data on the genetics, genomics and biology of the laboratory mouse. The mouse is an excellent and unique animal surrogate for studying normal development and disease processes in humans. Thus, MGD's primary goals are to facilitate the use of mouse models for studying human disease and enable the development of translational research hypotheses based on comparative genotype, phenotype and functional analyses. Core MGD data content includes gene characterization and functions, phenotype and disease model descriptions, DNA and protein sequence data, polymorphisms, gene mapping data and genome coordinates, and comparative gene data focused on mammals. Data are integrated from diverse sources, ranging from major resource centers to individual investigator laboratories and the scientific literature, using a combination of automated processes and expert human curation. MGD collaborates with the bioinformatics community on the development of data and semantic standards, and it incorporates key ontologies into the MGD annotation system, including the Gene Ontology (GO), the Mammalian Phenotype Ontology, and the Anatomical Dictionary for Mouse Development and the Adult Anatomy. MGD is the authoritative source for mouse nomenclature for genes, alleles, and mouse strains, and for GO annotations to mouse genes. MGD provides a unique platform for data mining and hypothesis generation where one can express complex queries simultaneously addressing phenotypic effects, biochemical function and process, sub-cellular location, expression, sequence, polymorphism and mapping data. Both web-based querying and computational access to data are provided. Recent improvements in MGD described here include the incorporation of single nucleotide polymorphism data and search tools, the addition of PIR gene superfamily classifications, phenotype data for NIH-acquired knockout mice, images for mouse phenotypic genotypes, new functional graph displays of GO annotations, and new orthology displays including sequence information and graphic displays

Drag'n Go: Simple and Fast Navigation in Virtual Environment

4 pages.International audienceIn this paper we introduce the Drag'n Go technique to navigate in multi-scale virtual 3d environment. This new technique takes its root from the point of interest (POI) approach where the user selects a target to reach. The biggest difference between the two is that with Drag'n Go the user keeps full control of its position relative to the target as well as its traveling speed. The technique requires only a 2d input and consequently, can be used with a large amount of devices like mouse, touch or pen screen. We conducted preliminary experiment that highlights that Drag'n Go is an efficient and appreciated method for touch-based device and a competitive approach for mouse-based device

Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site

We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. The gene sets were obtained from the functional Gene Ontology (GO) classification; for each set and motif we optimized the sequence similarity score threshold, independently for every location window (measured with respect to the TSS), taking into account the location dependent nucleotide heterogeneity along the promoters of the target genes. We performed a high throughput analysis, searching the promoters (from 200bp downstream to 1000bp upstream the TSS), of more than 8000 human and 23,000 mouse genes, for 134 functional Gene Ontology classes and for 412 known DNA motifs. When combined with binding site and location conservation between human and mouse, the method identifies with high probability functional binding sites that regulate groups of biologically related genes. We found many location-sensitive functional binding events and showed that they clustered close to the TSS. Our method and findings were put to several experimental tests. By allowing a "flexible" threshold and combining our functional class and location specific search method with conservation between human and mouse, we are able to identify reliably functional TF binding sites. This is an essential step towards constructing regulatory networks and elucidating the design principles that govern transcriptional regulation of expression. The promoter region proximal to the TSS appears to be of central importance for regulation of transcription in human and mouse, just as it is in bacteria and yeast.Comment: 31 pages, including Supplementary Information and figure

Mouse tracking to explore motor inhibition processes in go/no-go and stop signal tasks

Response inhibition relies on both proactive and reactive mechanisms that exert a synergic control on goal-directed actions. It is typically evaluated by the go/no-go (GNG) and the stop signal task (SST) with response recording based on the key-press method. However, the analysis of discrete variables (i.e., present or absent responses) registered by key-press could be insufficient to capture dynamic aspects of inhibitory control. Trying to overcome this limitation, in the present study we used a mouse tracking procedure to characterize movement profiles related to proactive and reactive inhibition. A total of fifty-three participants performed a cued GNG and an SST. The cued GNG mainly involves proactive control whereas the reactive component is mainly engaged in the SST. We evaluated the velocity profile from mouse trajectories both for responses obtained in the Go conditions and for inhibitory failures. Movements were classified as one-shot when no corrections were observed. Multi-peaked velocity profiles were classified as non-one-shot. A higher proportion of one-shot movements was found in the SST compared to the cued GNG when subjects failed to inhibit responses. This result suggests that proactive control may be responsible for unsmooth profiles in inhibition failures, supporting a differentiation between these tasks