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Nature Communications Apr 2019A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs...
A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of a broad set of current biological databases and the application of a robust analytical pipeline to produce readily interpretable results. Metascape is a web-based portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists. In terms of design features, Metascape combines functional enrichment, interactome analysis, gene annotation, and membership search to leverage over 40 independent knowledgebases within one integrated portal. Additionally, it facilitates comparative analyses of datasets across multiple independent and orthogonal experiments. Metascape provides a significantly simplified user experience through a one-click Express Analysis interface to generate interpretable outputs. Taken together, Metascape is an effective and efficient tool for experimental biologists to comprehensively analyze and interpret OMICs-based studies in the big data era.
Topics: Databases, Genetic; Genomics; Molecular Sequence Annotation; Orientation, Spatial; Software; Systems Biology; User-Computer Interface
PubMed: 30944313
DOI: 10.1038/s41467-019-09234-6 -
Frontiers in Neural Circuits 2020
Topics: Animals; Behavior; Humans; Motion Perception; Neurons; Orientation, Spatial; Space Perception
PubMed: 33324174
DOI: 10.3389/fncir.2020.619073 -
Annals of Physical and Rehabilitation... Jun 2017
Topics: Cognition; Humans; Orientation, Spatial; Space Perception
PubMed: 28606315
DOI: 10.1016/j.rehab.2017.05.003 -
The Journal of Experimental Biology Feb 2019Many casual observers typecast as a stationary pest that lurks around fruit and wine. However, the omnipresent fruit fly, which thrives even in desert habitats, likely... (Review)
Review
Many casual observers typecast as a stationary pest that lurks around fruit and wine. However, the omnipresent fruit fly, which thrives even in desert habitats, likely established and maintained its cosmopolitan status via migration over large spatial scales. To perform long-distance dispersal, flies must actively maintain a straight compass heading through the use of external orientation cues, such as those derived from the sky. In this Review, we address how accomplishes long-distance navigation using celestial cues. We focus on behavioral and physiological studies indicating that fruit flies can navigate both to a pattern of linearly polarized light and to the position of the sun - the same cues utilized by more heralded insect navigators such as monarch butterflies and desert ants. In both cases, fruit flies perform menotaxis, selecting seemingly arbitrary headings that they then maintain over time. We discuss how the fly's nervous system detects and processes this sensory information to direct the steering maneuvers that underlie navigation. In particular, we highlight recent findings that compass neurons in the central complex, a set of midline neuropils, are essential for navigation. Taken together, these results suggest that fruit flies share an ancient, latent capacity for celestial navigation with other insects. Furthermore, they illustrate the potential of to help us to elucidate both the cellular basis of navigation and mechanisms of directed dispersal on a landscape scale.
Topics: Animals; Cues; Drosophila melanogaster; Orientation, Spatial; Phototaxis; Spatial Navigation
PubMed: 30728228
DOI: 10.1242/jeb.186148 -
The Journal of Neuroscience : the... Feb 2022Narrowband γ oscillations (NBG: ∼20-60 Hz) in visual cortex reflect rhythmic fluctuations in population activity generated by underlying circuits tuned for stimulus...
Narrowband γ oscillations (NBG: ∼20-60 Hz) in visual cortex reflect rhythmic fluctuations in population activity generated by underlying circuits tuned for stimulus location, orientation, and color. A variety of theories posit a specific role for NBG in encoding and communicating this information within visual cortex. However, recent findings suggest a more nuanced role for NBG, given its dependence on certain stimulus feature configurations, such as coherent-oriented edges and specific hues. Motivated by these factors, we sought to quantify the independent and joint tuning properties of NBG to oriented and color stimuli using intracranial recordings from the human visual cortex (male and female). NBG was shown to display a cardinal orientation bias (horizontal) and also an end- and mid-spectral color bias (red/blue and green). When jointly probed, the cardinal bias for orientation was attenuated and an end-spectral preference for red and blue predominated. This loss of mid-spectral tuning occurred even for recording sites showing large responses to uniform green stimuli. Our results demonstrate the close, yet complex, link between the population dynamics driving NBG oscillations and known feature selectivity biases for orientation and color within visual cortex. Such a bias in stimulus tuning imposes new constraints on the functional significance of the visual γ rhythm. More generally, these biases in population electrophysiology will need to be considered in experiments using orientation or color features to examine the role of visual cortex in other domains, such as working memory and decision-making. Oscillations in electrophysiological activity occur in visual cortex in response to stimuli that strongly drive the orientation or color selectivity of visual neurons. The significance of this induced "γ rhythm" to brain function remains unclear. Answering this question requires understanding how and why some stimuli can reliably generate oscillatory γ activity while others do not. We examined how different orientations and colors independently and jointly modulate γ oscillations in the human brain. Our data show that γ oscillations are greatest for certain orientations and colors that reflect known response biases in visual cortex. Such findings complicate the functional significance of γ oscillations but open new avenues for linking circuits to population dynamics in visual cortex.
Topics: Adult; Color Perception; Electrocorticography; Female; Gamma Rhythm; Humans; Male; Middle Aged; Orientation, Spatial; Visual Cortex
PubMed: 34965979
DOI: 10.1523/JNEUROSCI.1085-21.2021 -
Journal of Vision Dec 2020Orientation perception is a fundamental property of the visual system and an important basic processing stage for visual scene perception. Neurophysiological studies...
Orientation perception is a fundamental property of the visual system and an important basic processing stage for visual scene perception. Neurophysiological studies have found broader tuning curves and increased noise in orientation-selective neurons of senescent monkeys and cats, results that suggest an age-related decline in orientation perception. However, behavioral studies in humans have found no evidence for such decline, with performance being comparable for younger and older participants in orientation detection and discrimination tasks. Crucially, previous behavioral studies assessed performance for cardinal orientation only, and it is well known that the human visual system prefers cardinal over oblique orientations, a phenomenon called the oblique effect. We hypothesized that age-related changes depend on the orientation tested. In two experiments, we investigated orientation discrimination and reproduction for a large range of cardinal and oblique orientations in younger and older adults. We found substantial age-related decline for oblique but not for cardinal orientations, thus demonstrating that orientation perception selectively declines for oblique orientations. Taken together, our results serve as the missing link between previous neurophysiological and human behavioral studies on orientation perception in healthy aging.
Topics: Adult; Aged; Aged, 80 and over; Aging; Female; Humans; Male; Middle Aged; Orientation, Spatial; Visual Perception; Young Adult
PubMed: 33351062
DOI: 10.1167/jov.20.13.13 -
Current Opinion in Neurology Feb 2024The vestibular system provides three-dimensional idiothetic cues for updating of one's position in space during head and body movement. Ascending vestibular signals... (Review)
Review
PURPOSE OF REVIEW
The vestibular system provides three-dimensional idiothetic cues for updating of one's position in space during head and body movement. Ascending vestibular signals reach entorhinal and hippocampal networks via head-direction pathways, where they converge with multisensory information to tune the place and grid cell code.
RECENT FINDINGS
Animal models have provided insight to neurobiological consequences of vestibular lesions for cerebral networks controlling spatial cognition. Multimodal cerebral imaging combined with behavioural testing of spatial orientation and navigation performance as well as strategy in the last years helped to decipher vestibular-cognitive interactions also in humans.
SUMMARY
This review will update the current knowledge on the anatomical and cellular basis of vestibular contributions to spatial orientation and navigation from a translational perspective (animal and human studies), delineate the behavioural and functional consequences of different vestibular pathologies on these cognitive domains, and will lastly speculate on a potential role of vestibular dysfunction for cognitive aging and impeding cognitive impairment in analogy to the well known effects of hearing loss.
Topics: Animals; Humans; Orientation, Spatial; Space Perception; Vestibule, Labyrinth; Cognition; Cues
PubMed: 38010039
DOI: 10.1097/WCO.0000000000001230 -
Annual Review of Neuroscience Jul 2017Diverse animals ranging from worms and insects to birds and turtles perform impressive journeys using the magnetic field of the earth as a cue. Although major cellular... (Review)
Review
Diverse animals ranging from worms and insects to birds and turtles perform impressive journeys using the magnetic field of the earth as a cue. Although major cellular and molecular mechanisms for sensing mechanical and chemical cues have been elucidated over the past three decades, the mechanisms that animals use to sense magnetic fields remain largely mysterious. Here we survey progress on the search for magnetosensory neurons and magnetosensitive molecules important for animal behaviors. Emphasis is placed on magnetosensation in insects and birds, as well as on the magnetosensitive neuron pair AFD in the nematode Caenorhabditis elegans. We also review conventional criteria used to define animal magnetoreceptors and suggest how approaches used to identify receptors for other sensory modalities may be adapted for magnetoreceptors. Finally, we discuss prospects for underutilized and novel approaches to identify the elusive magnetoreceptors in animals.
Topics: Animal Migration; Animals; Behavior, Animal; Magnetic Fields; Orientation, Spatial; Sensation
PubMed: 28772099
DOI: 10.1146/annurev-neuro-072116-031312 -
PeerJ 2023While extensive research has been advancing our understanding of the spatial and postural decline in healthy elderly (HE) and Alzheimer's disease (AD), much less is... (Review)
Review
BACKGROUND
While extensive research has been advancing our understanding of the spatial and postural decline in healthy elderly (HE) and Alzheimer's disease (AD), much less is known about how the vestibular system contributes to the spatial and postural processing in these two populations. This is especially relevant during turning movements in the dark, such as while walking in our garden or at home at night, where the vestibular signal becomes central. As the prevention of falls and disorientation are of serious concern for the medical service, more vestibular-driven knowledge is necessary to decrease the burden for HE and AD patients with vestibular disabilities.
OVERVIEW OF THE ARTICLE
The review briefly presents the current "non-vestibular based" knowledge (. knowledge based on research that does not mention the "vestibular system" as a contributor or does not investigate its effects) about spatial navigation and postural control during normal healthy ageing and AD pathology. Then, it concentrates on the critical sense of the vestibular system and explores the current expertise about the aspects of spatial orientation and postural control from a vestibular system point of view. The norm is set by first looking at how healthy elderly change with age with respect to their vestibular-guided navigation and balance, followed by the AD patients and the difficulties they experience in maintaining their balance or during navigation.
CONCLUSION
Vestibular spatial and vestibular postural deficits present a considerable disadvantage and are felt not only on a physical but also on a psychological level by all those affected. Still, there is a clear need for more (central) vestibular-driven spatial and postural knowledge in healthy and pathological ageing, which can better facilitate our understanding of the aetiology of these dysfunctions. A possible change can start with the more frequent implementation of the "vestibular system examination/rehabilitation/therapy" in the clinic, which can then lead to an improvement of future prognostication and disease outcome for the patients.
Topics: Aged; Humans; Alzheimer Disease; Orientation, Spatial; Postural Balance; Space Perception; Vestibule, Labyrinth
PubMed: 37151287
DOI: 10.7717/peerj.15040 -
Journal of Vision Feb 2021We examined whether perception of color saturation and lightness depends on the three-dimensional (3D) shape and surface gloss of surfaces rendered to have different...
We examined whether perception of color saturation and lightness depends on the three-dimensional (3D) shape and surface gloss of surfaces rendered to have different hues. In Experiment 1, we parametrically varied specular roughness of predominantly planar surfaces with different mesoscopic relief heights. The orientation of surfaces was varied relative to the light source and observer. Observers matched perceived lightness and chroma (effectively saturation) using spherical objects rendered using CIE LCH color space. We observed strong interactions between perceived saturation and lightness with changes in surface orientation and surface properties (specular roughness and 3D relief height). Declines in saturation and increases in lightness were observed with increasing specular roughness. Changes in relief height had greater effects on perceived saturation and lightness for blue hues compared with reddish and greenish hues. Experiment 2 found inverse correlations between perceived gloss and specular roughness across conditions. Experiment 3 estimated perceived specular coverage and found that a weighted combination of perceived gloss and specular coverage could account for perceived color saturation and lightness, with different coefficients accounting for the perceptual experience for each of the three hue conditions. These findings suggest that perceived color saturation and lightness depend on the separation of specular highlights from diffuse shading informative of chromatic surface reflectance.
Topics: Color Perception; Humans; Imaging, Three-Dimensional; Light; Orientation, Spatial; Surface Properties
PubMed: 33576764
DOI: 10.1167/jov.21.2.7