Action Control: Independent Effects of Memory and Monocular Viewing on Reaching Accuracy

ERIC Educational Resources Information Center

Westwood, D.A.; Robertson, C.; Heath, M.

2005-01-01

Evidence suggests that perceptual networks in the ventral visual pathway are necessary for action control when targets are viewed with only one eye, or when the target must be stored in memory. We tested whether memory-linked (i.e., open-loop versus memory-guided actions) and monocular-linked effects (i.e., binocular versus monocular actions) on…

Changes in Visual Object Recognition Precede the Shape Bias in Early Noun Learning

PubMed Central

Yee, Meagan; Jones, Susan S.; Smith, Linda B.

2012-01-01

Two of the most formidable skills that characterize human beings are language and our prowess in visual object recognition. They may also be developmentally intertwined. Two experiments, a large sample cross-sectional study and a smaller sample 6-month longitudinal study of 18- to 24-month-olds, tested a hypothesized developmental link between changes in visual object representation and noun learning. Previous findings in visual object recognition indicate that children’s ability to recognize common basic level categories from sparse structural shape representations of object shape emerges between the ages of 18 and 24 months, is related to noun vocabulary size, and is lacking in children with language delay. Other research shows in artificial noun learning tasks that during this same developmental period, young children systematically generalize object names by shape, that this shape bias predicts future noun learning, and is lacking in children with language delay. The two experiments examine the developmental relation between visual object recognition and the shape bias for the first time. The results show that developmental changes in visual object recognition systematically precede the emergence of the shape bias. The results suggest a developmental pathway in which early changes in visual object recognition that are themselves linked to category learning enable the discovery of higher-order regularities in category structure and thus the shape bias in novel noun learning tasks. The proposed developmental pathway has implications for understanding the role of specific experience in the development of both visual object recognition and the shape bias in early noun learning. PMID:23227015

TRPM1: the endpoint of the mGluR6 signal transduction cascade in retinal ON-bipolar cells.

PubMed

Morgans, Catherine W; Brown, Ronald Lane; Duvoisin, Robert M

2010-07-01

For almost 30 years the ion channel that initiates the ON visual pathway in vertebrate vision has remained elusive. Recent findings now indicate that the pathway, which begins with unbinding of glutamate from the metabotropic glutamate receptor 6 (mGluR6), ends with the opening of the transient receptor potential (TRP)M1 cation channel. As a component of the mGluR6 signal transduction pathway, mutations in TRPM1 would be expected to cause congenital stationary night blindness (CSNB), and several such mutations have already been identified in CSNB families. Furthermore, expression of TRPM1 in both the retina and skin raises the possibility that a genetic link exists between certain types of visual and skin disorders.

Visually based path-planning by Japanese monkeys.

PubMed

Mushiake, H; Saito, N; Sakamoto, K; Sato, Y; Tanji, J

2001-03-01

To construct an animal model of strategy formation, we designed a maze path-finding task. First, we asked monkeys to capture a goal in the maze by moving a cursor on the screen. Cursor movement was linked to movements of each wrist. When the animals learned the association between cursor movement and wrist movement, we established a start and a goal in the maze, and asked them to find a path between them. We found that the animals took the shortest pathway, rather than approaching the goal randomly. We further found that the animals adopted a strategy of selecting a fixed intermediate point in the visually presented maze to select one of the shortest pathways, suggesting a visually based path planning. To examine their capacity to use that strategy flexibly, we transformed the task by blocking pathways in the maze, providing a problem to solve. The animals then developed a strategy of solving the problem by planning a novel shortest path from the start to the goal and rerouting the path to bypass the obstacle.

International Practice in Care Provision for Post-stroke Visual Impairment.

PubMed

Rowe, Fiona J

2017-09-01

This study sought to explore the practice of orthoptists internationally in care provision for poststroke visual impairment. Survey questions were developed and piloted with clinicians, academics, and users. Questions addressed types of visual problems, how these were identified, treated, and followed up, care pathways in use, links with other professions, and referral options. The survey was approved by the institutional ethical committee. The survey was accessed via a web link that was circulated through the International Orthoptic Association member professional organisations to orthoptists. Completed electronic surveys were obtained from 299 individuals. About one-third (35.5%) of orthoptists saw patients within 2 weeks of stroke onset and over half (55.5%) by 1 month post stroke. Stroke survivors were routinely assessed by 87%; over three-quarters in eye clinics. Screening tools were used by 11%. Validated tests were used for assessment of visual acuity (76.5%), visual field (68.2%), eye movement (80.9%), binocular vision (77.9%), and visual function (55.8%). Visual problems suspected by family or professionals were high (86.6%). Typical overall follow-up period of vision care was less than 3 months. Designated care pathways for stroke survivors with visual problems were used by 56.9% of orthoptists. Information on visual impairment was provided by 85.9% of orthoptists. In international orthoptic practice, there is general agreement on assessment and management of visual impairment in stroke populations. More than half of orthoptists reported seeing stroke survivors within 1 month of the stroke onset, typically in eye clinics. There was a high use of validated tests of visual acuity, visual fields, ocular motility, and binocular vision. Similarly there was high use of established treatment options including prisms, occlusion, compensatory strategies, and oculomotor training, appropriately targeted at specific types of visual conditions/symptoms. This information can be used to inform choice of core outcome orthoptic measures in stroke practice.

A Review of the Benefits of Nature Experiences: More Than Meets the Eye.

PubMed

Franco, Lara S; Shanahan, Danielle F; Fuller, Richard A

2017-08-01

Evidence that experiences of nature can benefit people has accumulated rapidly. Yet perhaps because of the domination of the visual sense in humans, most research has focused on the visual aspects of nature experiences. However, humans are multisensory, and it seems likely that many benefits are delivered through the non-visual senses and these are potentially avenues through which a physiological mechanism could occur. Here we review the evidence around these lesser studied sensory pathways-through sound, smell, taste, touch, and three non-sensory pathways. Natural sounds and smells underpin experiences of nature for many people, and this may well be rooted in evolutionary psychology. Tactile experiences of nature, particularly beyond animal petting, are understudied yet potentially fundamentally important. Tastes of nature, through growing and consuming natural foods, have been linked with a range of health and well-being benefits. Beyond the five senses, evidence is emerging for other non-visual pathways for nature experiences to be effective. These include ingestion or inhalation of phytoncides, negative air ions and microbes. We conclude that (i) these non-visual avenues are potentially important for delivering benefits from nature experiences; (ii) the evidence base is relatively weak and often based on correlational studies; and (iii) deeper exploration of these sensory and non-sensory avenues is needed.

How can audiovisual pathways enhance the temporal resolution of time-compressed speech in blind subjects?

PubMed

Hertrich, Ingo; Dietrich, Susanne; Ackermann, Hermann

2013-01-01

In blind people, the visual channel cannot assist face-to-face communication via lipreading or visual prosody. Nevertheless, the visual system may enhance the evaluation of auditory information due to its cross-links to (1) the auditory system, (2) supramodal representations, and (3) frontal action-related areas. Apart from feedback or top-down support of, for example, the processing of spatial or phonological representations, experimental data have shown that the visual system can impact auditory perception at more basic computational stages such as temporal signal resolution. For example, blind as compared to sighted subjects are more resistant against backward masking, and this ability appears to be associated with activity in visual cortex. Regarding the comprehension of continuous speech, blind subjects can learn to use accelerated text-to-speech systems for "reading" texts at ultra-fast speaking rates (>16 syllables/s), exceeding by far the normal range of 6 syllables/s. A functional magnetic resonance imaging study has shown that this ability, among other brain regions, significantly covaries with BOLD responses in bilateral pulvinar, right visual cortex, and left supplementary motor area. Furthermore, magnetoencephalographic measurements revealed a particular component in right occipital cortex phase-locked to the syllable onsets of accelerated speech. In sighted people, the "bottleneck" for understanding time-compressed speech seems related to higher demands for buffering phonological material and is, presumably, linked to frontal brain structures. On the other hand, the neurophysiological correlates of functions overcoming this bottleneck, seem to depend upon early visual cortex activity. The present Hypothesis and Theory paper outlines a model that aims at binding these data together, based on early cross-modal pathways that are already known from various audiovisual experiments on cross-modal adjustments during space, time, and object recognition.

How can audiovisual pathways enhance the temporal resolution of time-compressed speech in blind subjects?

PubMed Central

Hertrich, Ingo; Dietrich, Susanne; Ackermann, Hermann

2013-01-01

In blind people, the visual channel cannot assist face-to-face communication via lipreading or visual prosody. Nevertheless, the visual system may enhance the evaluation of auditory information due to its cross-links to (1) the auditory system, (2) supramodal representations, and (3) frontal action-related areas. Apart from feedback or top-down support of, for example, the processing of spatial or phonological representations, experimental data have shown that the visual system can impact auditory perception at more basic computational stages such as temporal signal resolution. For example, blind as compared to sighted subjects are more resistant against backward masking, and this ability appears to be associated with activity in visual cortex. Regarding the comprehension of continuous speech, blind subjects can learn to use accelerated text-to-speech systems for “reading” texts at ultra-fast speaking rates (>16 syllables/s), exceeding by far the normal range of 6 syllables/s. A functional magnetic resonance imaging study has shown that this ability, among other brain regions, significantly covaries with BOLD responses in bilateral pulvinar, right visual cortex, and left supplementary motor area. Furthermore, magnetoencephalographic measurements revealed a particular component in right occipital cortex phase-locked to the syllable onsets of accelerated speech. In sighted people, the “bottleneck” for understanding time-compressed speech seems related to higher demands for buffering phonological material and is, presumably, linked to frontal brain structures. On the other hand, the neurophysiological correlates of functions overcoming this bottleneck, seem to depend upon early visual cortex activity. The present Hypothesis and Theory paper outlines a model that aims at binding these data together, based on early cross-modal pathways that are already known from various audiovisual experiments on cross-modal adjustments during space, time, and object recognition. PMID:23966968

Investigating the benefits of scene linking for a pathway HMD: from laboratory flight experiments to flight tests

NASA Astrophysics Data System (ADS)

Schmerwitz, Sven; Többen, Helmut; Lorenz, Bernd; Iijima, Tomoko; Kuritz-Kaiser, Anthea

2006-05-01

Pathway-in-the-sky displays enable pilots to accurately fly difficult trajectories. However, these displays may drive pilots' attention to the aircraft guidance task at the expense of other tasks particularly when the pathway display is located head-down. A pathway HUD may be a viable solution to overcome this disadvantage. Moreover, the pathway may mitigate the perceptual segregation between the static near domain and the dynamic far domain and hence, may improve attention switching between both sources. In order to more comprehensively overcome the perceptual near-to-far domain disconnect alphanumeric symbols could be attached to the pathway leading to a HUD design concept called 'scene-linking'. Two studies are presented that investigated this concept. The first study used a simplified laboratory flight experiment. Pilots (N=14) flew a curved trajectory through mountainous terrain and had to detect display events (discrete changes in a command speed indicator to be matched with current speed) and outside scene events (hostile SAM station on ground). The speed indicators were presented in superposition to the scenery either in fixed position or scene-linked to the pathway. Outside scene event detection was found improved with scene linking, however, flight-path tracking was markedly deteriorated. In the second study a scene-linked pathway concept was implemented on a monocular retinal scanning HMD and tested in real flights on a Do228 involving 5 test pilots. The flight test mainly focused at usability issues of the display in combination with an optical head tracker. Visual and instrument departure and approach tasks were evaluated comparing HMD navigation with standard instrument or terrestrial navigation. The study revealed limitations of the HMD regarding its see-through capability, field of view, weight and wearing comfort that showed to have a strong influence on pilot acceptance rather than rebutting the approach of the display concept as such.

PathText: a text mining integrator for biological pathway visualizations

PubMed Central

Kemper, Brian; Matsuzaki, Takuya; Matsuoka, Yukiko; Tsuruoka, Yoshimasa; Kitano, Hiroaki; Ananiadou, Sophia; Tsujii, Jun'ichi

2010-01-01

Motivation: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists construct a pathway by reading a large number of articles and interpreting them as a consistent network, but most of the models constructed currently lack direct links to those articles. Biologists who want to check the original articles have to spend substantial amounts of time to collect relevant articles and identify the sections relevant to the pathway. Furthermore, with the scientific literature expanding by several thousand papers per week, keeping a model relevant requires a continuous curation effort. In this article, we present a system designed to integrate a pathway visualizer, text mining systems and annotation tools into a seamless environment. This will enable biologists to freely move between parts of a pathway and relevant sections of articles, as well as identify relevant papers from large text bases. The system, PathText, is developed by Systems Biology Institute, Okinawa Institute of Science and Technology, National Centre for Text Mining (University of Manchester) and the University of Tokyo, and is being used by groups of biologists from these locations. Contact: brian@monrovian.com. PMID:20529930

A tale of two agnosias: distinctions between form and integrative agnosia.

PubMed

Riddoch, M Jane; Humphreys, Glyn W; Akhtar, Nabeela; Allen, Harriet; Bracewell, R Martyn; Schofield, Andrew J

2008-02-01

The performance of two patients with visual agnosia was compared across a number of tests examining visual processing. The patients were distinguished by having dorsal and medial ventral extrastriate lesions. While inanimate objects were disadvantaged for the patient with a dorsal extrastriate lesion, animate items are disadvantaged for the patient with the medial ventral extrastriate lesion. The patients also showed contrasting patterns of performance on the Navon Test: The patient with a dorsal extrastriate lesion demonstrated a local bias while the patient with a medial ventral extrastriate lesion had a global bias. We propose that the dorsal and medial ventral visual pathways may be characterized at an extrastriate level by differences in local relative to more global visual processing and that this can link to visually based category-specific deficits in processing.

Electron-beam generated porous dextran gels: experimental and quantum chemical studies.

PubMed

Naumov, Sergej; Knolle, Wolfgang; Becher, Jana; Schnabelrauch, Matthias; Reichelt, Senta

2014-06-01

The aim of this work was to investigate the reaction mechanism of electron-beam generated macroporous dextran cryogels by quantum chemical calculation and electron paramagnetic resonance measurements. Electron-beam radiation was used to initiate the cross-linking reaction of methacrylated dextran in semifrozen aqueous solutions. The pore morphology of the resulting cryogels was visualized by scanning electron microscopy. Quantum chemical calculations and electron paramagnetic resonance studies provided information on the most probable reaction pathway and the chain growth radicals. The most probable reaction pathway was a ring opening reaction and the addition of a C-atom to the double-bond of the methacrylated dextran molecule. First detailed quantum chemical calculation on the reaction mechanism of electron-beam initiated cross-linking reaction of methacrylated dextran are presented.

Experimental induction of reading difficulties in normal readers provides novel insights into the neurofunctional mechanisms of visual word recognition.

PubMed

Heim, Stefan; Weidner, Ralph; von Overheidt, Ann-Christin; Tholen, Nicole; Grande, Marion; Amunts, Katrin

2014-03-01

Phonological and visual dysfunctions may result in reading deficits like those encountered in developmental dyslexia. Here, we use a novel approach to induce similar reading difficulties in normal readers in an event-related fMRI study, thus systematically investigating which brain regions relate to different pathways relating to orthographic-phonological (e.g. grapheme-to-phoneme conversion, GPC) vs. visual processing. Based upon a previous behavioural study (Tholen et al. 2011), the retrieval of phonemes from graphemes was manipulated by lowering the identifiability of letters in familiar vs. unfamiliar shapes. Visual word and letter processing was impeded by presenting the letters of a word in a moving, non-stationary manner. FMRI revealed that the visual condition activated cytoarchitectonically defined area hOC5 in the magnocellular pathway and area 7A in the right mesial parietal cortex. In contrast, the grapheme manipulation revealed different effects localised predominantly in bilateral inferior frontal gyrus (left cytoarchitectonic area 44; right area 45) and inferior parietal lobule (including areas PF/PFm), regions that have been demonstrated to show abnormal activation in dyslexic as compared to normal readers. This pattern of activation bears close resemblance to recent findings in dyslexic samples both behaviourally and with respect to the neurofunctional activation patterns. The novel paradigm may thus prove useful in future studies to understand reading problems related to distinct pathways, potentially providing a link also to the understanding of real reading impairments in dyslexia.

From genes to brain oscillations: is the visual pathway the epigenetic clue to schizophrenia?

PubMed

González-Hernández, J A; Pita-Alcorta, C; Cedeño, I R

2006-01-01

Molecular data and gene expression data and recently mitochondrial genes and possible epigenetic regulation by non-coding genes is revolutionizing our views on schizophrenia. Genes and epigenetic mechanisms are triggered by cell-cell interaction and by external stimuli. A number of recent clinical and molecular observations indicate that epigenetic factors may be operational in the origin of the illness. Based on the molecular insights, gene expression profiles and epigenetic regulation of gene, we went back to the neurophysiology (brain oscillations) and found a putative role of the visual experiences (i.e. visual stimuli) as epigenetic factor. The functional evidences provided here, establish a direct link between the striate and extrastriate unimodal visual cortex and the neurobiology of the schizophrenia. This result support the hypothesis that 'visual experience' has a potential role as epigenetic factor and contribute to trigger and/or to maintain the progression of the schizophrenia. In this case, candidate genes sensible for the visual 'insult' may be located within the visual cortex including associative areas, while the integrity of the visual pathway before reaching the primary visual cortex is preserved. The same effect can be perceived if target genes are localised within the visual pathway, which actually, is more sensitive for 'insult' during the early life than the cortex per se. If this process affects gene expression at these sites a stably sensory specific 'insult', i.e. distorted visual information, is entering the visual system and expanded to fronto-temporo-parietal multimodal areas even from early maturation periods. The difference in the timing of postnatal neuroanatomical events between such areas and the primary visual cortex in humans (with the formers reaching the same development landmarks later in life than the latter) is 'optimal' to establish an abnormal 'cell- communication' mediated by the visual system that may further interfere with the local physiology. In this context the strategy to search target genes need to be rearrangement and redirected to visual-related genes. Otherwise, psychophysics studies combining functional neuroimage, and electrophysiology are strongly recommended, for the search of epigenetic clues that will allow to carrier gene association studies in schizophrenia.

Brainstem origins for cortical 'what' and 'where' pathways in the auditory system.

PubMed

Kraus, Nina; Nicol, Trent

2005-04-01

We have developed a data-driven conceptual framework that links two areas of science: the source-filter model of acoustics and cortical sensory processing streams. The source-filter model describes the mechanics behind speech production: the identity of the speaker is carried largely in the vocal cord source and the message is shaped by the ever-changing filters of the vocal tract. Sensory processing streams, popularly called 'what' and 'where' pathways, are well established in the visual system as a neural scheme for separately carrying different facets of visual objects, namely their identity and their position/motion, to the cortex. A similar functional organization has been postulated in the auditory system. Both speaker identity and the spoken message, which are simultaneously conveyed in the acoustic structure of speech, can be disentangled into discrete brainstem response components. We argue that these two response classes are early manifestations of auditory 'what' and 'where' streams in the cortex. This brainstem link forges a new understanding of the relationship between the acoustics of speech and cortical processing streams, unites two hitherto separate areas in science, and provides a model for future investigations of auditory function.

Patterns of Individual Variation in Visual Pathway Structure and Function in the Sighted and Blind

PubMed Central

Datta, Ritobrato; Benson, Noah C.; Prasad, Sashank; Jacobson, Samuel G.; Cideciyan, Artur V.; Bridge, Holly; Watkins, Kate E.; Butt, Omar H.; Dain, Aleksandra S.; Brandes, Lauren; Gennatas, Efstathios D.

2016-01-01

Many structural and functional brain alterations accompany blindness, with substantial individual variation in these effects. In normally sighted people, there is correlated individual variation in some visual pathway structures. Here we examined if the changes in brain anatomy produced by blindness alter the patterns of anatomical variation found in the sighted. We derived eight measures of central visual pathway anatomy from a structural image of the brain from 59 sighted and 53 blind people. These measures showed highly significant differences in mean size between the sighted and blind cohorts. When we examined the measurements across individuals within each group we found three clusters of correlated variation, with V1 surface area and pericalcarine volume linked, and independent of the thickness of V1 cortex. These two clusters were in turn relatively independent of the volumes of the optic chiasm and lateral geniculate nucleus. This same pattern of variation in visual pathway anatomy was found in the sighted and the blind. Anatomical changes within these clusters were graded by the timing of onset of blindness, with those subjects with a post-natal onset of blindness having alterations in brain anatomy that were intermediate to those seen in the sighted and congenitally blind. Many of the blind and sighted subjects also contributed functional MRI measures of cross-modal responses within visual cortex, and a diffusion tensor imaging measure of fractional anisotropy within the optic radiations and the splenium of the corpus callosum. We again found group differences between the blind and sighted in these measures. The previously identified clusters of anatomical variation were also found to be differentially related to these additional measures: across subjects, V1 cortical thickness was related to cross-modal activation, and the volume of the optic chiasm and lateral geniculate was related to fractional anisotropy in the visual pathway. Our findings show that several of the structural and functional effects of blindness may be reduced to a smaller set of dimensions. It also seems that the changes in the brain that accompany blindness are on a continuum with normal variation found in the sighted. PMID:27812129

A Review of the Benefits of Nature Experiences: More Than Meets the Eye

PubMed Central

Franco, Lara S.; Shanahan, Danielle F.

2017-01-01

Evidence that experiences of nature can benefit people has accumulated rapidly. Yet perhaps because of the domination of the visual sense in humans, most research has focused on the visual aspects of nature experiences. However, humans are multisensory, and it seems likely that many benefits are delivered through the non-visual senses and these are potentially avenues through which a physiological mechanism could occur. Here we review the evidence around these lesser studied sensory pathways—through sound, smell, taste, touch, and three non-sensory pathways. Natural sounds and smells underpin experiences of nature for many people, and this may well be rooted in evolutionary psychology. Tactile experiences of nature, particularly beyond animal petting, are understudied yet potentially fundamentally important. Tastes of nature, through growing and consuming natural foods, have been linked with a range of health and well-being benefits. Beyond the five senses, evidence is emerging for other non-visual pathways for nature experiences to be effective. These include ingestion or inhalation of phytoncides, negative air ions and microbes. We conclude that (i) these non-visual avenues are potentially important for delivering benefits from nature experiences; (ii) the evidence base is relatively weak and often based on correlational studies; and (iii) deeper exploration of these sensory and non-sensory avenues is needed. PMID:28763021

MetExploreViz: web component for interactive metabolic network visualization.

PubMed

Chazalviel, Maxime; Frainay, Clément; Poupin, Nathalie; Vinson, Florence; Merlet, Benjamin; Gloaguen, Yoann; Cottret, Ludovic; Jourdan, Fabien

2017-09-15

MetExploreViz is an open source web component that can be easily embedded in any web site. It provides features dedicated to the visualization of metabolic networks and pathways and thus offers a flexible solution to analyze omics data in a biochemical context. Documentation and link to GIT code repository (GPL 3.0 license)are available at this URL: http://metexplore.toulouse.inra.fr/metexploreViz/doc /. Tutorial is available at this URL. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Recurrent V1-V2 interaction in early visual boundary processing.

PubMed

Neumann, H; Sepp, W

1999-11-01

A majority of cortical areas are connected via feedforward and feedback fiber projections. In feedforward pathways we mainly observe stages of feature detection and integration. The computational role of the descending pathways at different stages of processing remains mainly unknown. Based on empirical findings we suggest that the top-down feedback pathways subserve a context-dependent gain control mechanism. We propose a new computational model for recurrent contour processing in which normalized activities of orientation selective contrast cells are fed forward to the next processing stage. There, the arrangement of input activation is matched against local patterns of contour shape. The resulting activities are subsequently fed back to the previous stage to locally enhance those initial measurements that are consistent with the top-down generated responses. In all, we suggest a computational theory for recurrent processing in the visual cortex in which the significance of local measurements is evaluated on the basis of a broader visual context that is represented in terms of contour code patterns. The model serves as a framework to link physiological with perceptual data gathered in psychophysical experiments. It handles a variety of perceptual phenomena, such as the local grouping of fragmented shape outline, texture surround and density effects, and the interpolation of illusory contours.

Visual navigation in adolescents with early periventricular lesions: knowing where, but not getting there.

PubMed

Pavlova, Marina; Sokolov, Alexander; Krägeloh-Mann, Ingeborg

2007-02-01

Visual navigation in familiar and unfamiliar surroundings is an essential ingredient of adaptive daily life behavior. Recent brain imaging work helps to recognize that establishing connectivity between brain regions is of importance for successful navigation. Here, we ask whether the ability to navigate is impaired in adolescents who were born premature and suffer congenital bilateral periventricular brain damage that might affect the pathways interconnecting subcortical structures with cortex. Performance on a set of visual labyrinth tasks was significantly worse in patients with periventricular leukomalacia (PVL) as compared with premature-born controls without lesions and term-born adolescents. The ability for visual navigation inversely relates to the severity of motor disability, leg-dominated bilateral spastic cerebral palsy. This agrees with the view that navigation ability substantially improves with practice and might be compromised in individuals with restrictions in active spatial exploration. Visual navigation is negatively linked to the volumetric extent of lesions over the right parietal and frontal periventricular regions. Whereas impairments of visual processing of point-light biological motion are associated in patients with PVL with bilateral parietal periventricular lesions, navigation ability is specifically linked to the frontal lesions in the right hemisphere. We suggest that more anterior periventricular lesions impair the interrelations between the right hippocampus and cortical areas leading to disintegration of neural networks engaged in visual navigation. For the first time, we show that the severity of right frontal periventricular damage and leg-dominated motor disorders can serve as independent predictors of the visual navigation disability.

Neural correlates of visualizations of concrete and abstract words in preschool children: a developmental embodied approach

PubMed Central

D’Angiulli, Amedeo; Griffiths, Gordon; Marmolejo-Ramos, Fernando

2015-01-01

The neural correlates of visualization underlying word comprehension were examined in preschool children. On each trial, a concrete or abstract word was delivered binaurally (part 1: post-auditory visualization), followed by a four-picture array (a target plus three distractors; part 2: matching visualization). Children were to select the picture matching the word they heard in part 1. Event-related potentials (ERPs) locked to each stimulus presentation and task interval were averaged over sets of trials of increasing word abstractness. ERP time-course during both parts of the task showed that early activity (i.e., <300 ms) was predominant in response to concrete words, while activity in response to abstract words became evident only at intermediate (i.e., 300–699 ms) and late (i.e., 700–1000 ms) ERP intervals. Specifically, ERP topography showed that while early activity during post-auditory visualization was linked to left temporo-parietal areas for concrete words, early activity during matching visualization occurred mostly in occipito-parietal areas for concrete words, but more anteriorly in centro-parietal areas for abstract words. In intermediate ERPs, post-auditory visualization coincided with parieto-occipital and parieto-frontal activity in response to both concrete and abstract words, while in matching visualization a parieto-central activity was common to both types of words. In the late ERPs for both types of words, the post-auditory visualization involved right-hemispheric activity following a “post-anterior” pathway sequence: occipital, parietal, and temporal areas; conversely, matching visualization involved left-hemispheric activity following an “ant-posterior” pathway sequence: frontal, temporal, parietal, and occipital areas. These results suggest that, similarly, for concrete and abstract words, meaning in young children depends on variably complex visualization processes integrating visuo-auditory experiences and supramodal embodying representations. PMID:26175697

A micro-level model of employment relations and health inequalities.

PubMed

Benach, Joan; Solar, Orielle; Santana, Vilma; Castedo, Antía; Chung, Haejoo; Muntaner, Carles

2010-01-01

Theoretical models are a way of visualizing, in context, the many factors that contribute to inequalities in health. This article presents a model showing the micro-level pathways relating employment and working conditions to health inequalities. A first important (indirect) pathway runs through the unequal distribution of harmful working conditions. Both employment and working conditions tend to be unequally distributed along the same social axes: social class, gender, ethnicity/race, immigration/migration status, territory, and so forth. Underlying mechanisms are exploitation, domination, and discrimination. Material deprivation and economic inequalities constitute a second direct pathway linking (nonstandard) employment conditions to health inequalities. In a third pathway, employment conditions may have an important effect on health inequalities via several psychosocial, behavioral, and physiopathological pathways. Although these several pathways are separated for analytical purposes, they are largely intertwined and, ideally, should be studied in an integrated way. The theoretical model presented in this article serves three main purposes: providing analytical clarity for organizing scientific data, encouraging further observation and causal testing, and identifying policy entry points.

Neural pathways for visual speech perception

PubMed Central

Bernstein, Lynne E.; Liebenthal, Einat

2014-01-01

This paper examines the questions, what levels of speech can be perceived visually, and how is visual speech represented by the brain? Review of the literature leads to the conclusions that every level of psycholinguistic speech structure (i.e., phonetic features, phonemes, syllables, words, and prosody) can be perceived visually, although individuals differ in their abilities to do so; and that there are visual modality-specific representations of speech qua speech in higher-level vision brain areas. That is, the visual system represents the modal patterns of visual speech. The suggestion that the auditory speech pathway receives and represents visual speech is examined in light of neuroimaging evidence on the auditory speech pathways. We outline the generally agreed-upon organization of the visual ventral and dorsal pathways and examine several types of visual processing that might be related to speech through those pathways, specifically, face and body, orthography, and sign language processing. In this context, we examine the visual speech processing literature, which reveals widespread diverse patterns of activity in posterior temporal cortices in response to visual speech stimuli. We outline a model of the visual and auditory speech pathways and make several suggestions: (1) The visual perception of speech relies on visual pathway representations of speech qua speech. (2) A proposed site of these representations, the temporal visual speech area (TVSA) has been demonstrated in posterior temporal cortex, ventral and posterior to multisensory posterior superior temporal sulcus (pSTS). (3) Given that visual speech has dynamic and configural features, its representations in feedforward visual pathways are expected to integrate these features, possibly in TVSA. PMID:25520611

Curvature-processing network in macaque visual cortex

PubMed Central

Yue, Xiaomin; Pourladian, Irene S.; Tootell, Roger B. H.; Ungerleider, Leslie G.

2014-01-01

Our visual environment abounds with curved features. Thus, the goal of understanding visual processing should include the processing of curved features. Using functional magnetic resonance imaging in behaving monkeys, we demonstrated a network of cortical areas selective for the processing of curved features. This network includes three distinct hierarchically organized regions within the ventral visual pathway: a posterior curvature-biased patch (PCP) located in the near-foveal representation of dorsal V4, a middle curvature-biased patch (MCP) located on the ventral lip of the posterior superior temporal sulcus (STS) in area TEO, and an anterior curvature-biased patch (ACP) located just below the STS in anterior area TE. Our results further indicate that the processing of curvature becomes increasingly complex from PCP to ACP. The proximity of the curvature-processing network to the well-known face-processing network suggests a possible functional link between them. PMID:25092328

Distinct GABAergic targets of feedforward and feedback connections between lower and higher areas of rat visual cortex.

PubMed

Gonchar, Yuri; Burkhalter, Andreas

2003-11-26

Processing of visual information is performed in different cortical areas that are interconnected by feedforward (FF) and feedback (FB) pathways. Although FF and FB inputs are excitatory, their influences on pyramidal neurons also depend on the outputs of GABAergic neurons, which receive FF and FB inputs. Rat visual cortex contains at least three different families of GABAergic neurons that express parvalbumin (PV), calretinin (CR), and somatostatin (SOM) (Gonchar and Burkhalter, 1997). To examine whether pathway-specific inhibition (Shao and Burkhalter, 1996) is attributable to distinct connections with GABAergic neurons, we traced FF and FB inputs to PV, CR, and SOM neurons in layers 1-2/3 of area 17 and the secondary lateromedial area in rat visual cortex. We found that in layer 2/3 maximally 2% of FF and FB inputs go to CR and SOM neurons. This contrasts with 12-13% of FF and FB inputs onto layer 2/3 PV neurons. Unlike inputs to layer 2/3, connections to layer 1, which contains CR but lacks SOM and PV somata, are pathway-specific: 21% of FB inputs go to CR neurons, whereas FF inputs to layer 1 and its CR neurons are absent. These findings suggest that FF and FB influences on layer 2/3 pyramidal neurons mainly involve disynaptic connections via PV neurons that control the spike outputs to axons and proximal dendrites. Unlike FF input, FB input in addition makes a disynaptic link via CR neurons, which may influence the excitability of distal pyramidal cell dendrites in layer 1.

Magnocellular-dorsal pathway and sub-lexical route in developmental dyslexia

PubMed Central

Gori, Simone; Cecchini, Paolo; Bigoni, Anna; Molteni, Massimo; Facoetti, Andrea

2014-01-01

Although developmental dyslexia (DD) is frequently associate with a phonological deficit, the underlying neurobiological cause remains undetermined. Recently, a new model, called “temporal sampling framework” (TSF), provided an innovative prospect in the DD study. TSF suggests that deficits in syllabic perception at a specific temporal frequencies are the critical basis for the poor reading performance in DD. This approach was presented as a possible neurobiological substrate of the phonological deficit of DD but the TSF can also easily be applied to the visual modality deficits. The deficit in the magnocellular-dorsal (M-D) pathway - often found in individuals with DD - fits well with a temporal oscillatory deficit specifically related to this visual pathway. This study investigated the visual M-D and parvocellular-ventral (P-V) pathways in dyslexic and in chronological age and IQ-matched normally reading children by measuring temporal (frequency doubling illusion) and static stimuli sensitivity, respectively. A specific deficit in M-D temporal oscillation was found. Importantly, the M-D deficit was selectively shown in poor phonological decoders. M-D deficit appears to be frequent because 75% of poor pseudo-word readers were at least 1 SD below the mean of the controls. Finally, a replication study by using a new group of poor phonological decoders and reading level controls suggested a crucial role of M-D deficit in DD. These results showed that a M-D deficit might impair the sub-lexical mechanisms that are critical for reading development. The possible link between these findings and TSF is discussed. PMID:25009484

Metabolic Pathways Visualization Skills Development by Undergraduate Students

ERIC Educational Resources Information Center

dos Santos, Vanessa J. S. V.; Galembeck, Eduardo

2015-01-01

We have developed a metabolic pathways visualization skill test (MPVST) to gain greater insight into our students' abilities to comprehend the visual information presented in metabolic pathways diagrams. The test is able to discriminate students' visualization ability with respect to six specific visualization skills that we identified as key to…

Personalized Guideline-Based Treatment Recommendations Using Natural Language Processing Techniques.

PubMed

Becker, Matthias; Böckmann, Britta

2017-01-01

Clinical guidelines and clinical pathways are accepted and proven instruments for quality assurance and process optimization. Today, electronic representation of clinical guidelines exists as unstructured text, but is not well-integrated with patient-specific information from electronic health records. Consequently, generic content of the clinical guidelines is accessible, but it is not possible to visualize the position of the patient on the clinical pathway, decision support cannot be provided by personalized guidelines for the next treatment step. The Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) provides common reference terminology as well as the semantic link for combining the pathways and the patient-specific information. This paper proposes a model-based approach to support the development of guideline-compliant pathways combined with patient-specific structured and unstructured information using SNOMED CT. To identify SNOMED CT concepts, a software was developed to extract SNOMED CT codes out of structured and unstructured German data to map these with clinical pathways annotated in accordance with the systematized nomenclature.

Clinical implications of parallel visual pathways.

PubMed

Bassi, C J; Lehmkuhle, S

1990-02-01

Visual information travels from the retina to visual cortical areas along at least two parallel pathways. In this paper, anatomical and physiological evidence is presented to demonstrate the existence of, and trace these two pathways throughout the visual systems of the cat, primate, and human. Physiological and behavioral experiments are discussed which establish that these two pathways are differentially sensitive to stimuli that vary in spatial and temporal frequency. One pathway (M-pathway) is more sensitive to coarse visual form that is modulated or moving at fast rates, whereas the other pathway (P-pathway) is more sensitive to spatial detail that is stationary or moving at slow rates. This difference between the M- and P-pathways is related to some spatial and temporal effects observed in humans. Furthermore, evidence is presented that certain diseases selectively comprise the functioning of M- or P-pathways (i.e., glaucoma, Alzheimer's disease, and anisometropic amblyopia), and some of the spatial and temporal deficits observed in these patients are presented within the context of the dysfunction of the M- or P-pathway.

Altered white matter in early visual pathways of humans with amblyopia.

PubMed

Allen, Brian; Spiegel, Daniel P; Thompson, Benjamin; Pestilli, Franco; Rokers, Bas

2015-09-01

Amblyopia is a visual disorder caused by poorly coordinated binocular input during development. Little is known about the impact of amblyopia on the white matter within the visual system. We studied the properties of six major visual white-matter pathways in a group of adults with amblyopia (n=10) and matched controls (n=10) using diffusion weighted imaging (DWI) and fiber tractography. While we did not find significant differences in diffusion properties in cortico-cortical pathways, patients with amblyopia exhibited increased mean diffusivity in thalamo-cortical visual pathways. These findings suggest that amblyopia may systematically alter the white matter properties of early visual pathways. Copyright © 2015 Elsevier Ltd. All rights reserved.

Audio-visual integration through the parallel visual pathways.

PubMed

Kaposvári, Péter; Csete, Gergő; Bognár, Anna; Csibri, Péter; Tóth, Eszter; Szabó, Nikoletta; Vécsei, László; Sáry, Gyula; Tamás Kincses, Zsigmond

2015-10-22

Audio-visual integration has been shown to be present in a wide range of different conditions, some of which are processed through the dorsal, and others through the ventral visual pathway. Whereas neuroimaging studies have revealed integration-related activity in the brain, there has been no imaging study of the possible role of segregated visual streams in audio-visual integration. We set out to determine how the different visual pathways participate in this communication. We investigated how audio-visual integration can be supported through the dorsal and ventral visual pathways during the double flash illusion. Low-contrast and chromatic isoluminant stimuli were used to drive preferably the dorsal and ventral pathways, respectively. In order to identify the anatomical substrates of the audio-visual interaction in the two conditions, the psychophysical results were correlated with the white matter integrity as measured by diffusion tensor imaging.The psychophysiological data revealed a robust double flash illusion in both conditions. A correlation between the psychophysical results and local fractional anisotropy was found in the occipito-parietal white matter in the low-contrast condition, while a similar correlation was found in the infero-temporal white matter in the chromatic isoluminant condition. Our results indicate that both of the parallel visual pathways may play a role in the audio-visual interaction. Copyright © 2015. Published by Elsevier B.V.

Dystrophin Is Required for Proper Functioning of Luminance and Red-Green Cone Opponent Mechanisms in the Human Retina.

PubMed

Barboni, Mirella Telles Salgueiro; Martins, Cristiane Maria Gomes; Nagy, Balázs Vince; Tsai, Tina; Damico, Francisco Max; da Costa, Marcelo Fernandes; de Cassia, Rita; Pavanello, M; Lourenço, Naila Cristina Vilaça; de Cerqueira, Antonia Maria Pereira; Zatz, Mayana; Kremers, Jan; Ventura, Dora Fix

2016-07-01

Visual information is processed in parallel pathways in the visual system. Parallel processing begins at the synapse between the photoreceptors and their postreceptoral neurons in the human retina. The integrity of this first neural connection is vital for normal visual processing downstream. Of the numerous elements necessary for proper functioning of this synaptic contact, dystrophin proteins in the eye play an important role. Deficiency of muscle dystrophin causes Duchenne muscular dystrophy (DMD), an X-linked disease that affects muscle function and leads to decreased life expectancy. In DMD patients, postreceptoral retinal mechanisms underlying scotopic and photopic vision and ON- and OFF-pathway responses are also altered. In this study, we recorded the electroretinogram (ERG) while preferentially activating the (red-green) opponent or the luminance pathway, and compared data from healthy participants (n = 16) with those of DMD patients (n = 10). The stimuli were heterochromatic sinusoidal modulations at a mean luminance of 200 cd/m2. The recordings allowed us also to analyze ON and OFF cone-driven retinal responses. We found significant differences in 12-Hz response amplitudes and phases between controls and DMD patients, with conditions with large luminance content resulting in larger response amplitudes in DMD patients compared to controls, whereas responses of DMD patients were smaller when pure chromatic modulation was given. The results suggest that dystrophin is required for the proper function of luminance and red-green cone opponent mechanisms in the human retina.

Goal-Directed Visual Processing Differentially Impacts Human Ventral and Dorsal Visual Representations

PubMed Central

2017-01-01

Recent studies have challenged the ventral/“what” and dorsal/“where” two-visual-processing-pathway view by showing the existence of “what” and “where” information in both pathways. Is the two-pathway distinction still valid? Here, we examined how goal-directed visual information processing may differentially impact visual representations in these two pathways. Using fMRI and multivariate pattern analysis, in three experiments on human participants (57% females), by manipulating whether color or shape was task-relevant and how they were conjoined, we examined shape-based object category decoding in occipitotemporal and parietal regions. We found that object category representations in all the regions examined were influenced by whether or not object shape was task-relevant. This task effect, however, tended to decrease as task-relevant and irrelevant features were more integrated, reflecting the well-known object-based feature encoding. Interestingly, task relevance played a relatively minor role in driving the representational structures of early visual and ventral object regions. They were driven predominantly by variations in object shapes. In contrast, the effect of task was much greater in dorsal than ventral regions, with object category and task relevance both contributing significantly to the representational structures of the dorsal regions. These results showed that, whereas visual representations in the ventral pathway are more invariant and reflect “what an object is,” those in the dorsal pathway are more adaptive and reflect “what we do with it.” Thus, despite the existence of “what” and “where” information in both visual processing pathways, the two pathways may still differ fundamentally in their roles in visual information representation. SIGNIFICANCE STATEMENT Visual information is thought to be processed in two distinctive pathways: the ventral pathway that processes “what” an object is and the dorsal pathway that processes “where” it is located. This view has been challenged by recent studies revealing the existence of “what” and “where” information in both pathways. Here, we found that goal-directed visual information processing differentially modulates shape-based object category representations in the two pathways. Whereas ventral representations are more invariant to the demand of the task, reflecting what an object is, dorsal representations are more adaptive, reflecting what we do with the object. Thus, despite the existence of “what” and “where” information in both pathways, visual representations may still differ fundamentally in the two pathways. PMID:28821655

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

DOE Office of Scientific and Technical Information (OSTI.GOV)

King, Zachary A.; Drager, Andreas; Ebrahim, Ali

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics).more » Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.« less

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

PubMed Central

King, Zachary A.; Dräger, Andreas; Ebrahim, Ali; Sonnenschein, Nikolaus; Lewis, Nathan E.; Palsson, Bernhard O.

2015-01-01

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics). Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools. PMID:26313928

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

DOE PAGES

King, Zachary A.; Drager, Andreas; Ebrahim, Ali; ...

2015-08-27

Escher is a web application for visualizing data on biological pathways. Three key features make Escher a uniquely effective tool for pathway visualization. First, users can rapidly design new pathway maps. Escher provides pathway suggestions based on user data and genome-scale models, so users can draw pathways in a semi-automated way. Second, users can visualize data related to genes or proteins on the associated reactions and pathways, using rules that define which enzymes catalyze each reaction. Thus, users can identify trends in common genomic data types (e.g. RNA-Seq, proteomics, ChIP)—in conjunction with metabolite- and reaction-oriented data types (e.g. metabolomics, fluxomics).more » Third, Escher harnesses the strengths of web technologies (SVG, D3, developer tools) so that visualizations can be rapidly adapted, extended, shared, and embedded. This paper provides examples of each of these features and explains how the development approach used for Escher can be used to guide the development of future visualization tools.« less

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

PubMed Central

Gao, Jianjiong; Aksoy, Bülent Arman; Dogrusoz, Ugur; Dresdner, Gideon; Gross, Benjamin; Sumer, S. Onur; Sun, Yichao; Jacobsen, Anders; Sinha, Rileen; Larsson, Erik; Cerami, Ethan; Sander, Chris; Schultz, Nikolaus

2014-01-01

The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics. PMID:23550210

The neurobiological basis of seeing words

PubMed Central

Wandell, Brian A.

2011-01-01

This review summarizes recent ideas about the cortical circuits for seeing words, an important part of the brain system for reading. Historically, the link between the visual cortex and reading has been contentious. One influential position is that the visual cortex plays a minimal role, limited to identifying contours, and that information about these contours is delivered to cortical regions specialized for reading and language. An alternative position is that specializations for seeing words develop within the visual cortex itself. Modern neuroimaging measurements—including both functional magnetic resonance imaging (fMRI) and diffusion weighted imaging with tractography data—support the position that circuitry for seeing the statistical regularities of word forms develops within the ventral occipitotemporal cortex, which also contains important circuitry for seeing faces, colors, and forms. The review explains new findings about the visual pathways, including visual field maps, as well as new findings about how we see words. The measurements from the two fields are in close cortical proximity, and there are good opportunities for coordinating theoretical ideas about function in the ventral occipitotemporal cortex. PMID:21486296

The neurobiological basis of seeing words.

PubMed

Wandell, Brian A

2011-04-01

This review summarizes recent ideas about the cortical circuits for seeing words, an important part of the brain system for reading. Historically, the link between the visual cortex and reading has been contentious. One influential position is that the visual cortex plays a minimal role, limited to identifying contours, and that information about these contours is delivered to cortical regions specialized for reading and language. An alternative position is that specializations for seeing words develop within the visual cortex itself. Modern neuroimaging measurements-including both functional magnetic resonance imaging (fMRI) and diffusion weighted imaging with tractography (DTI) data-support the position that circuitry for seeing the statistical regularities of word forms develops within the ventral occipitotemporal cortex, which also contains important circuitry for seeing faces, colors, and forms. This review explains new findings about the visual pathways, including visual field maps, as well as new findings about how we see words. The measurements from the two fields are in close cortical proximity, and there are good opportunities for coordinating theoretical ideas about function in the ventral occipitotemporal cortex. © 2011 New York Academy of Sciences.

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

PubMed

Slenter, Denise N; Kutmon, Martina; Hanspers, Kristina; Riutta, Anders; Windsor, Jacob; Nunes, Nuno; Mélius, Jonathan; Cirillo, Elisa; Coort, Susan L; Digles, Daniela; Ehrhart, Friederike; Giesbertz, Pieter; Kalafati, Marianthi; Martens, Marvin; Miller, Ryan; Nishida, Kozo; Rieswijk, Linda; Waagmeester, Andra; Eijssen, Lars M T; Evelo, Chris T; Pico, Alexander R; Willighagen, Egon L

2018-01-04

WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

PubMed Central

Caspi, Ron; Altman, Tomer; Dale, Joseph M.; Dreher, Kate; Fulcher, Carol A.; Gilham, Fred; Kaipa, Pallavi; Karthikeyan, Athikkattuvalasu S.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Mueller, Lukas A.; Paley, Suzanne; Popescu, Liviu; Pujar, Anuradha; Shearer, Alexander G.; Zhang, Peifen; Karp, Peter D.

2010-01-01

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism. PMID:19850718

Corynebacterium diphtheriae methionine sulfoxide reductase a exploits a unique mycothiol redox relay mechanism.

PubMed

Tossounian, Maria-Armineh; Pedre, Brandán; Wahni, Khadija; Erdogan, Huriye; Vertommen, Didier; Van Molle, Inge; Messens, Joris

2015-05-01

Methionine sulfoxide reductases are conserved enzymes that reduce oxidized methionines in proteins and play a pivotal role in cellular redox signaling. We have unraveled the redox relay mechanisms of methionine sulfoxide reductase A of the pathogen Corynebacterium diphtheriae (Cd-MsrA) and shown that this enzyme is coupled to two independent redox relay pathways. Steady-state kinetics combined with mass spectrometry of Cd-MsrA mutants give a view of the essential cysteine residues for catalysis. Cd-MsrA combines a nucleophilic cysteine sulfenylation reaction with an intramolecular disulfide bond cascade linked to the thioredoxin pathway. Within this cascade, the oxidative equivalents are transferred to the surface of the protein while releasing the reduced substrate. Alternatively, MsrA catalyzes methionine sulfoxide reduction linked to the mycothiol/mycoredoxin-1 pathway. After the nucleophilic cysteine sulfenylation reaction, MsrA forms a mixed disulfide with mycothiol, which is transferred via a thiol disulfide relay mechanism to a second cysteine for reduction by mycoredoxin-1. With x-ray crystallography, we visualize two essential intermediates of the thioredoxin relay mechanism and a cacodylate molecule mimicking the substrate interactions in the active site. The interplay of both redox pathways in redox signaling regulation forms the basis for further research into the oxidative stress response of this pathogen. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Neuronal mechanisms underlying differences in spatial resolution between darks and lights in human vision.

PubMed

Pons, Carmen; Mazade, Reece; Jin, Jianzhong; Dul, Mitchell W; Zaidi, Qasim; Alonso, Jose-Manuel

2017-12-01

Artists and astronomers noticed centuries ago that humans perceive dark features in an image differently from light ones; however, the neuronal mechanisms underlying these dark/light asymmetries remained unknown. Based on computational modeling of neuronal responses, we have previously proposed that such perceptual dark/light asymmetries originate from a luminance/response saturation within the ON retinal pathway. Consistent with this prediction, here we show that stimulus conditions that increase ON luminance/response saturation (e.g., dark backgrounds) or its effect on light stimuli (e.g., optical blur) impair the perceptual discrimination and salience of light targets more than dark targets in human vision. We also show that, in cat visual cortex, the magnitude of the ON luminance/response saturation remains relatively constant under a wide range of luminance conditions that are common indoors, and only shifts away from the lowest luminance contrasts under low mesopic light. Finally, we show that the ON luminance/response saturation affects visual salience mostly when the high spatial frequencies of the image are reduced by poor illumination or optical blur. Because both low luminance and optical blur are risk factors in myopia, our results suggest a possible neuronal mechanism linking myopia progression with the function of the ON visual pathway.

Neuronal mechanisms underlying differences in spatial resolution between darks and lights in human vision

PubMed Central

Pons, Carmen; Mazade, Reece; Jin, Jianzhong; Dul, Mitchell W.; Zaidi, Qasim; Alonso, Jose-Manuel

2017-01-01

Artists and astronomers noticed centuries ago that humans perceive dark features in an image differently from light ones; however, the neuronal mechanisms underlying these dark/light asymmetries remained unknown. Based on computational modeling of neuronal responses, we have previously proposed that such perceptual dark/light asymmetries originate from a luminance/response saturation within the ON retinal pathway. Consistent with this prediction, here we show that stimulus conditions that increase ON luminance/response saturation (e.g., dark backgrounds) or its effect on light stimuli (e.g., optical blur) impair the perceptual discrimination and salience of light targets more than dark targets in human vision. We also show that, in cat visual cortex, the magnitude of the ON luminance/response saturation remains relatively constant under a wide range of luminance conditions that are common indoors, and only shifts away from the lowest luminance contrasts under low mesopic light. Finally, we show that the ON luminance/response saturation affects visual salience mostly when the high spatial frequencies of the image are reduced by poor illumination or optical blur. Because both low luminance and optical blur are risk factors in myopia, our results suggest a possible neuronal mechanism linking myopia progression with the function of the ON visual pathway. PMID:29196762

Functional and structural comparison of visual lateralization in birds – similar but still different

PubMed Central

Ströckens, Felix

2014-01-01

Vertebrate brains display physiological and anatomical left-right differences, which are related to hemispheric dominances for specific functions. Functional lateralizations likely rely on structural left-right differences in intra- and interhemispheric connectivity patterns that develop in tight gene-environment interactions. The visual systems of chickens and pigeons show that asymmetrical light stimulation during ontogeny induces a dominance of the left hemisphere for visuomotor control that is paralleled by projection asymmetries within the ascending visual pathways. But structural asymmetries vary essentially between both species concerning the affected pathway (thalamo- vs. tectofugal system), constancy of effects (transient vs. permanent), and the hemisphere receiving stronger bilateral input (right vs. left). These discrepancies suggest that at least two aspects of visual processes are influenced by asymmetric light stimulation: (1) visuomotor dominance develops within the ontogenetically stronger stimulated hemisphere but not necessarily in the one receiving stronger bottom-up input. As a secondary consequence of asymmetrical light experience, lateralized top-down mechanisms play a critical role in the emergence of hemispheric dominance. (2) Ontogenetic light experiences may affect the dominant use of left- and right-hemispheric strategies. Evidences from social and spatial cognition tasks indicate that chickens rely more on a right-hemispheric global strategy whereas pigeons display a dominance of the left hemisphere. Thus, behavioral asymmetries are linked to a stronger bilateral input to the right hemisphere in chickens but to the left one in pigeons. The degree of bilateral visual input may determine the dominant visual processing strategy when redundant encoding is possible. This analysis supports that environmental stimulation affects the balance between hemispheric-specific processing by lateralized interactions of bottom-up and top-down systems. PMID:24723898

Implicit integration in a case of integrative visual agnosia.

PubMed

Aviezer, Hillel; Landau, Ayelet N; Robertson, Lynn C; Peterson, Mary A; Soroker, Nachum; Sacher, Yaron; Bonneh, Yoram; Bentin, Shlomo

2007-05-15

We present a case (SE) with integrative visual agnosia following ischemic stroke affecting the right dorsal and the left ventral pathways of the visual system. Despite his inability to identify global hierarchical letters [Navon, D. (1977). Forest before trees: The precedence of global features in visual perception. Cognitive Psychology, 9, 353-383], and his dense object agnosia, SE showed normal global-to-local interference when responding to local letters in Navon hierarchical stimuli and significant picture-word identity priming in a semantic decision task for words. Since priming was absent if these features were scrambled, it stands to reason that these effects were not due to priming by distinctive features. The contrast between priming effects induced by coherent and scrambled stimuli is consistent with implicit but not explicit integration of features into a unified whole. We went on to show that possible/impossible object decisions were facilitated by words in a word-picture priming task, suggesting that prompts could activate perceptually integrated images in a backward fashion. We conclude that the absence of SE's ability to identify visual objects except through tedious serial construction reflects a deficit in accessing an integrated visual representation through bottom-up visual processing alone. However, top-down generated images can help activate these visual representations through semantic links.

Abnormal white matter tractography of visual pathways detected by high-angular-resolution diffusion imaging (HARDI) corresponds to visual dysfunction in cortical/cerebral visual impairment

PubMed Central

Bauer, Corinna M.; Heidary, Gena; Koo, Bang-Bon; Killiany, Ronald J.; Bex, Peter; Merabet, Lotfi B.

2014-01-01

Cortical (cerebral) visual impairment (CVI) is characterized by visual dysfunction associated with damage to the optic radiations and/or visual cortex. Typically it results from pre- or perinatal hypoxic damage to postchiasmal visual structures and pathways. The neuroanatomical basis of this condition remains poorly understood, particularly with regard to how the resulting maldevelopment of visual processing pathways relates to observations in the clinical setting. We report our investigation of 2 young adults diagnosed with CVI and visual dysfunction characterized by difficulties related to visually guided attention and visuospatial processing. Using high-angular-resolution diffusion imaging (HARDI), we characterized and compared their individual white matter projections of the extrageniculo-striate visual system with a normal-sighted control. Compared to a sighted control, both CVI cases revealed a striking reduction in association fibers, including the inferior frontal-occipital fasciculus as well as superior and inferior longitudinal fasciculi. This reduction in fibers associated with the major pathways implicated in visual processing may provide a neuroanatomical basis for the visual dysfunctions observed in these patients. PMID:25087644

I'll take the low road: the evolutionary underpinnings of visually triggered fear

PubMed Central

Carr, James A.

2015-01-01

Although there is general agreement that the central nucleus of the amygdala (CeA) is critical for triggering the neuroendocrine response to visual threats, there is uncertainty about the role of subcortical visual pathways in this process. Primates in general appear to depend less on subcortical visual pathways than other mammals. Yet, imaging studies continue to indicate a role for the superior colliculus and pulvinar nucleus in fear activation, despite disconnects in how these brain structures communicate not only with each other but with the amygdala. Studies in fish and amphibians suggest that the neuroendocrine response to visual threats has remained relatively unchanged for hundreds of millions of years, yet there are still significant data gaps with respect to how visual information is relayed to telencephalic areas homologous to the CeA, particularly in fish. In fact ray finned fishes may have evolved an entirely different mechanism for relaying visual information to the telencephalon. In part because they lack a pathway homologous to the lateral geniculate-striate cortex pathway of mammals, amphibians continue to be an excellent model for studying how stress hormones in turn modulate fear activating visual pathways. Glucocorticoids, melanocortin peptides, and CRF all appear to play some role in modulating sensorimotor processing in the optic tectum. These observations, coupled with data showing control of the hypothalamus-pituitary-adrenal axis by the superior colliculus, suggest a fear/stress/anxiety neuroendocrine circuit that begins with first order synapses in subcortical visual pathways. Thus, comparative studies shed light not only on how fear triggering visual pathways came to be, but how hormones released as a result of this activation modulate these pathways. PMID:26578871

Plasticity of the human visual system after retinal gene therapy in patients with Leber’s congenital amaurosis

PubMed Central

Ashtari, Manzar; Zhang, Hui; Cook, Philip A.; Cyckowski, Laura L.; Shindler, Kenneth S.; Marshall, Kathleen A.; Aravand, Puya; Vossough, Arastoo; Gee, James C.; Maguire, Albert M.; Baker, Chris I.; Bennett, Jean

2015-01-01

Much of our knowledge of the mechanisms underlying plasticity in the visual cortex in response to visual impairment, vision restoration, and environmental interactions comes from animal studies. We evaluated human brain plasticity in a group of patients with Leber’s congenital amaurosis (LCA), who regained vision through gene therapy. Using non-invasive multimodal neuroimaging methods, we demonstrated that reversing blindness with gene therapy promoted long-term structural plasticity in the visual pathways emanating from the treated retina of LCA patients. The data revealed improvements and normalization along the visual fibers corresponding to the site of retinal injection of the gene therapy vector carrying the therapeutic gene in the treated eye compared to the visual pathway for the untreated eye of LCA patients. After gene therapy, the primary visual pathways (for example, geniculostriate fibers) in the treated retina were similar to those of sighted control subjects, whereas the primary visual pathways of the untreated retina continued to deteriorate. Our results suggest that visual experience, enhanced by gene therapy, may be responsible for the reorganization and maturation of synaptic connectivity in the visual pathways of the treated eye in LCA patients. The interactions between the eye and the brain enabled improved and sustained long-term visual function in patients with LCA after gene therapy. PMID:26180100

PathFinder: reconstruction and dynamic visualization of metabolic pathways.

PubMed

Goesmann, Alexander; Haubrock, Martin; Meyer, Folker; Kalinowski, Jörn; Giegerich, Robert

2002-01-01

Beyond methods for a gene-wise annotation and analysis of sequenced genomes new automated methods for functional analysis on a higher level are needed. The identification of realized metabolic pathways provides valuable information on gene expression and regulation. Detection of incomplete pathways helps to improve a constantly evolving genome annotation or discover alternative biochemical pathways. To utilize automated genome analysis on the level of metabolic pathways new methods for the dynamic representation and visualization of pathways are needed. PathFinder is a tool for the dynamic visualization of metabolic pathways based on annotation data. Pathways are represented as directed acyclic graphs, graph layout algorithms accomplish the dynamic drawing and visualization of the metabolic maps. A more detailed analysis of the input data on the level of biochemical pathways helps to identify genes and detect improper parts of annotations. As an Relational Database Management System (RDBMS) based internet application PathFinder reads a list of EC-numbers or a given annotation in EMBL- or Genbank-format and dynamically generates pathway graphs.

MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity

PubMed Central

2012-01-01

Background Exposure to environmental tobacco smoke (ETS) leads to higher rates of pulmonary diseases and infections in children. To study the biochemical changes that may precede lung diseases, metabolomic effects on fetal and maternal lungs and plasma from rats exposed to ETS were compared to filtered air control animals. Genome- reconstructed metabolic pathways may be used to map and interpret dysregulation in metabolic networks. However, mass spectrometry-based non-targeted metabolomics datasets often comprise many metabolites for which links to enzymatic reactions have not yet been reported. Hence, network visualizations that rely on current biochemical databases are incomplete and also fail to visualize novel, structurally unidentified metabolites. Results We present a novel approach to integrate biochemical pathway and chemical relationships to map all detected metabolites in network graphs (MetaMapp) using KEGG reactant pair database, Tanimoto chemical and NIST mass spectral similarity scores. In fetal and maternal lungs, and in maternal blood plasma from pregnant rats exposed to environmental tobacco smoke (ETS), 459 unique metabolites comprising 179 structurally identified compounds were detected by gas chromatography time of flight mass spectrometry (GC-TOF MS) and BinBase data processing. MetaMapp graphs in Cytoscape showed much clearer metabolic modularity and complete content visualization compared to conventional biochemical mapping approaches. Cytoscape visualization of differential statistics results using these graphs showed that overall, fetal lung metabolism was more impaired than lungs and blood metabolism in dams. Fetuses from ETS-exposed dams expressed lower lipid and nucleotide levels and higher amounts of energy metabolism intermediates than control animals, indicating lower biosynthetic rates of metabolites for cell division, structural proteins and lipids that are critical for in lung development. Conclusions MetaMapp graphs efficiently visualizes mass spectrometry based metabolomics datasets as network graphs in Cytoscape, and highlights metabolic alterations that can be associated with higher rate of pulmonary diseases and infections in children prenatally exposed to ETS. The MetaMapp scripts can be accessed at http://metamapp.fiehnlab.ucdavis.edu. PMID:22591066

Glycinergic Pathways of the Central Auditory System and Adjacent Reticular Formation of the Rat.

NASA Astrophysics Data System (ADS)

Hunter, Chyren

The development of techniques to visualize and identify specific transmitters of neuronal circuits has stimulated work on the characterization of pathways in the rat central nervous system that utilize the inhibitory amino acid glycine as its neurotransmitter. Glycine is a major inhibitory transmitter in the spinal cord and brainstem of vertebrates where it satisfies the major criteria for neurotransmitter action. Some of these characteristics are: uneven distribution in brain, high affinity reuptake mechanisms, inhibitory neurophysiological actions on certain neuronal populations, uneven receptor distribution and the specific antagonism of its actions by the convulsant alkaloid strychnine. Behaviorally, antagonism of glycinergic neurotransmission in the medullary reticular formation is linked to the development of myoclonus and seizures which may be initiated by auditory as well as other stimuli. In the present study, decreases in the concentration of glycine as well as the density of glycine receptors in the medulla with aging were found and may be responsible for the lowered threshold for strychnine seizures observed in older rats. Neuroanatomical pathways in the central auditory system and medullary and pontine reticular formation (RF) were investigated using retrograde transport of tritiated glycine to identify glycinergic pathways; immunohistochemical techniques were used to corroborate the location of glycine neurons. Within the central auditory system, retrograde transport studies using tritiated glycine demonstrated an ipsilateral glycinergic pathway linking nuclei of the ascending auditory system. This pathway has its cell bodies in the medial nucleus of the trapezoid body (MNTB) and projects to the ventrocaudal division of the ventral nucleus of the lateral lemniscus (VLL). Collaterals of this glycinergic projection terminate in the ipsilateral lateral superior olive (LSO). Other glycinergic pathways found were afferent to the VLL and have their origin in the ventral and lateral nuclei of the trapezoid body (MVPO and LVPO). Bilateral projections from the nucleus reticularis pontis oralis (RPOo), to the VLL were also identified as glycinergic. This projection may link motor output systems to ascending auditory input, generating the auditory behavioral responses seen with glycine antagonism in animal models of myoclonus and seizure.

New pharmacologic approaches to treating diabetic retinopathy.

PubMed

Ryan, Gina J

2007-09-01

The goal of treatment of diabetic retinopathy, limitations of laser photocoagulation, endpoints used in clinical studies of diabetic retinopathy treatments, and the mechanism of action, efficacy, and safety of several new and emerging therapies targeting the biochemical pathways that link chronic hyperglycemia with microvascular damage in patients with diabetic retinopathy are discussed. Improving or preserving vision is the primary goal of treatment for diabetic retinopathy. Limitations of laser photocoagulation include a lack of efficacy in some cases, discomfort from the procedure, the need for repeated treatment, and a risk of retinal damage and scarring. Visual acuity, quality of life, and macular thickness are used as endpoints in clinical studies of diabetic retinopathy treatments. Microvascular damage in patients with chronic hyperglycemia is mediated by interrelated pathways involving aldose reductase, advanced glycation end products, protein kinase C (PKC), and vascular endothelial growth factor (VEGF). Oral aldose reductase inhibitors have been studied with some success only in patients with diabetic peripheral neuropathy. The oral PKC inhibitor midostaurin and oral selective PKC beta inhibitor ruboxistaurin appear promising for improving or maintaining visual acuity, with gastrointestinal complaints the most commonly reported adverse effects. Intra-vitreal injection of corticosteroids or VEGF inhibitors is associated with short-lived improvement in or maintenance of visual acuity, a need for repeated injection, and a risk of local adverse effects. A variety of promising new therapies for diabetic retinopathy targeting the biochemical pathways that cause microvascular damage are under investigation. Additional clinical research is needed to determine the role of these new therapies in treating diabetic retinopathy.

Comparative study of visual pathways in owls (Aves: Strigiformes).

PubMed

Gutiérrez-Ibáñez, Cristián; Iwaniuk, Andrew N; Lisney, Thomas J; Wylie, Douglas R

2013-01-01

Although they are usually regarded as nocturnal, owls exhibit a wide range of activity patterns, from strictly nocturnal, to crepuscular or cathemeral, to diurnal. Several studies have shown that these differences in the activity pattern are reflected in differences in eye morphology and retinal organization. Despite the evidence that differences in activity pattern among owl species are reflected in the peripheral visual system, there has been no attempt to correlate these differences with changes in the visual regions in the brain. In this study, we compare the relative size of nuclei in the main visual pathways in nine species of owl that exhibit a wide range of activity patterns. We found marked differences in the relative size of all visual structures among the species studied, both in the tectofugal and the thalamofugal pathway, as well in other retinorecipient nuclei, including the nucleus lentiformis mesencephali, the nucleus of the basal optic root and the nucleus geniculatus lateralis, pars ventralis. We show that the barn owl (Tyto alba), a species widely used in the study of the integration of visual and auditory processing, has reduced visual pathways compared to strigid owls. Our results also suggest there could be a trade-off between the relative size of visual pathways and auditory pathways, similar to that reported in mammals. Finally, our results show that although there is no relationship between activity pattern and the relative size of either the tectofugal or the thalamofugal pathway, there is a positive correlation between the relative size of both visual pathways and the relative number of cells in the retinal ganglion layer. Copyright © 2012 S. Karger AG, Basel.

Reading impairment in schizophrenia: dysconnectivity within the visual system.

PubMed

Vinckier, Fabien; Cohen, Laurent; Oppenheim, Catherine; Salvador, Alexandre; Picard, Hernan; Amado, Isabelle; Krebs, Marie-Odile; Gaillard, Raphaël

2014-01-01

Patients with schizophrenia suffer from perceptual visual deficits. It remains unclear whether those deficits result from an isolated impairment of a localized brain process or from a more diffuse long-range dysconnectivity within the visual system. We aimed to explore, with a reading paradigm, the functioning of both ventral and dorsal visual pathways and their interaction in schizophrenia. Patients with schizophrenia and control subjects were studied using event-related functional MRI (fMRI) while reading words that were progressively degraded through word rotation or letter spacing. Reading intact or minimally degraded single words involves mainly the ventral visual pathway. Conversely, reading in non-optimal conditions involves both the ventral and the dorsal pathway. The reading paradigm thus allowed us to study the functioning of both pathways and their interaction. Behaviourally, patients with schizophrenia were selectively impaired at reading highly degraded words. While fMRI activation level was not different between patients and controls, functional connectivity between the ventral and dorsal visual pathways increased with word degradation in control subjects, but not in patients. Moreover, there was a negative correlation between the patients' behavioural sensitivity to stimulus degradation and dorso-ventral connectivity. This study suggests that perceptual visual deficits in schizophrenia could be related to dysconnectivity between dorsal and ventral visual pathways. © 2013 Published by Elsevier Ltd.

Parallel neural pathways in higher visual centers of the Drosophila brain that mediate wavelength-specific behavior

PubMed Central

Otsuna, Hideo; Shinomiya, Kazunori; Ito, Kei

2014-01-01

Compared with connections between the retinae and primary visual centers, relatively less is known in both mammals and insects about the functional segregation of neural pathways connecting primary and higher centers of the visual processing cascade. Here, using the Drosophila visual system as a model, we demonstrate two levels of parallel computation in the pathways that connect primary visual centers of the optic lobe to computational circuits embedded within deeper centers in the central brain. We show that a seemingly simple achromatic behavior, namely phototaxis, is under the control of several independent pathways, each of which is responsible for navigation towards unique wavelengths. Silencing just one pathway is enough to disturb phototaxis towards one characteristic monochromatic source, whereas phototactic behavior towards white light is not affected. The response spectrum of each demonstrable pathway is different from that of individual photoreceptors, suggesting subtractive computations. A choice assay between two colors showed that these pathways are responsible for navigation towards, but not for the detection itself of, the monochromatic light. The present study provides novel insights about how visual information is separated and processed in parallel to achieve robust control of an innate behavior. PMID:24574974

Cholinergic enhancement of visual attention and neural oscillations in the human brain.

PubMed

Bauer, Markus; Kluge, Christian; Bach, Dominik; Bradbury, David; Heinze, Hans Jochen; Dolan, Raymond J; Driver, Jon

2012-03-06

Cognitive processes such as visual perception and selective attention induce specific patterns of brain oscillations. The neurochemical bases of these spectral changes in neural activity are largely unknown, but neuromodulators are thought to regulate processing. The cholinergic system is linked to attentional function in vivo, whereas separate in vitro studies show that cholinergic agonists induce high-frequency oscillations in slice preparations. This has led to theoretical proposals that cholinergic enhancement of visual attention might operate via gamma oscillations in visual cortex, although low-frequency alpha/beta modulation may also play a key role. Here we used MEG to record cortical oscillations in the context of administration of a cholinergic agonist (physostigmine) during a spatial visual attention task in humans. This cholinergic agonist enhanced spatial attention effects on low-frequency alpha/beta oscillations in visual cortex, an effect correlating with a drug-induced speeding of performance. By contrast, the cholinergic agonist did not alter high-frequency gamma oscillations in visual cortex. Thus, our findings show that cholinergic neuromodulation enhances attentional selection via an impact on oscillatory synchrony in visual cortex, for low rather than high frequencies. We discuss this dissociation between high- and low-frequency oscillations in relation to proposals that lower-frequency oscillations are generated by feedback pathways within visual cortex. Copyright © 2012 Elsevier Ltd. All rights reserved.

Anomalous visual experiences, negative symptoms, perceptual organization and the magnocellular pathway in schizophrenia: a shared construct?

PubMed

Kéri, Szabolcs; Kiss, Imre; Kelemen, Oguz; Benedek, György; Janka, Zoltán

2005-10-01

Schizophrenia is associated with impaired visual information processing. The aim of this study was to investigate the relationship between anomalous perceptual experiences, positive and negative symptoms, perceptual organization, rapid categorization of natural images and magnocellular (M) and parvocellular (P) visual pathway functioning. Thirty-five unmedicated patients with schizophrenia and 20 matched healthy control volunteers participated. Anomalous perceptual experiences were assessed with the Bonn Scale for the Assessment Basic Symptoms (BSABS). General intellectual functions were evaluated with the revised version of the Wechsler Adult Intelligence Scale. The 1-9 version of the Continuous Performance Test (CPT) was used to investigate sustained attention. The following psychophysical tests were used: detection of Gabor patches with collinear and orthogonal flankers (perceptual organization), categorization of briefly presented natural scenes (rapid visual processing), low-contrast and frequency-doubling vernier threshold (M pathway functioning), isoluminant colour vernier threshold and high spatial frequency discrimination (P pathway functioning). The patients with schizophrenia were impaired on test of perceptual organization, rapid visual processing and M pathway functioning. There was a significant correlation between BSABS scores, negative symptoms, perceptual organization, rapid visual processing and M pathway functioning. Positive symptoms, IQ, CPT and P pathway measures did not correlate with these parameters. The best predictor of the BSABS score was the perceptual organization deficit. These results raise the possibility that multiple facets of visual information processing deficits can be explained by M pathway dysfunctions in schizophrenia, resulting in impaired attentional modulation of perceptual organization and of natural image categorization.

Cerebral Visual Impairment: Which Perceptive Visual Dysfunctions Can Be Expected in Children with Brain Damage? A Systematic Review

ERIC Educational Resources Information Center

Boot, F. H.; Pel, J. J. M.; van der Steen, J.; Evenhuis, H. M.

2010-01-01

The current definition of Cerebral Visual Impairment (CVI) includes all visual dysfunctions caused by damage to, or malfunctioning of, the retrochiasmatic visual pathways in the absence of damage to the anterior visual pathways or any major ocular disease. CVI is diagnosed by exclusion and the existence of many different causes and symptoms make…

Plasticity of the human visual system after retinal gene therapy in patients with Leber's congenital amaurosis.

PubMed

Ashtari, Manzar; Zhang, Hui; Cook, Philip A; Cyckowski, Laura L; Shindler, Kenneth S; Marshall, Kathleen A; Aravand, Puya; Vossough, Arastoo; Gee, James C; Maguire, Albert M; Baker, Chris I; Bennett, Jean

2015-07-15

Much of our knowledge of the mechanisms underlying plasticity in the visual cortex in response to visual impairment, vision restoration, and environmental interactions comes from animal studies. We evaluated human brain plasticity in a group of patients with Leber's congenital amaurosis (LCA), who regained vision through gene therapy. Using non-invasive multimodal neuroimaging methods, we demonstrated that reversing blindness with gene therapy promoted long-term structural plasticity in the visual pathways emanating from the treated retina of LCA patients. The data revealed improvements and normalization along the visual fibers corresponding to the site of retinal injection of the gene therapy vector carrying the therapeutic gene in the treated eye compared to the visual pathway for the untreated eye of LCA patients. After gene therapy, the primary visual pathways (for example, geniculostriate fibers) in the treated retina were similar to those of sighted control subjects, whereas the primary visual pathways of the untreated retina continued to deteriorate. Our results suggest that visual experience, enhanced by gene therapy, may be responsible for the reorganization and maturation of synaptic connectivity in the visual pathways of the treated eye in LCA patients. The interactions between the eye and the brain enabled improved and sustained long-term visual function in patients with LCA after gene therapy. Copyright © 2015, American Association for the Advancement of Science.

Mining gene link information for survival pathway hunting.

PubMed

Jing, Gao-Jian; Zhang, Zirui; Wang, Hong-Qiang; Zheng, Hong-Mei

2015-08-01

This study proposes a gene link-based method for survival time-related pathway hunting. In this method, the authors incorporate gene link information to estimate how a pathway is associated with cancer patient's survival time. Specifically, a gene link-based Cox proportional hazard model (Link-Cox) is established, in which two linked genes are considered together to represent a link variable and the association of the link with survival time is assessed using Cox proportional hazard model. On the basis of the Link-Cox model, the authors formulate a new statistic for measuring the association of a pathway with survival time of cancer patients, referred to as pathway survival score (PSS), by summarising survival significance over all the gene links in the pathway, and devise a permutation test to test the significance of an observed PSS. To evaluate the proposed method, the authors applied it to simulation data and two publicly available real-world gene expression data sets. Extensive comparisons with previous methods show the effectiveness and efficiency of the proposed method for survival pathway hunting.

Chromatic and achromatic visual fields in relation to choroidal thickness in patients with high myopia: A pilot study.

PubMed

García-Domene, M C; Luque, M J; Díez-Ajenjo, M A; Desco-Esteban, M C; Artigas, J M

2018-02-01

To analyse the relationship between the choroidal thickness and the visual perception of patients with high myopia but without retinal damage. All patients underwent ophthalmic evaluation including a slit lamp examination and dilated ophthalmoscopy, subjective refraction, best corrected visual acuity, axial length, optical coherence tomography, contrast sensitivity function and sensitivity of the visual pathways. We included eleven eyes of subjects with high myopia. There are statistical correlations between choroidal thickness and almost all the contrast sensitivity values. The sensitivity of magnocellular and koniocellular pathways is the most affected, and the homogeneity of the sensibility of the magnocellular pathway depends on the choroidal thickness; when the thickness decreases, the sensitivity impairment extends from the center to the periphery of the visual field. Patients with high myopia without any fundus changes have visual impairments. We have found that choroidal thickness correlates with perceptual parameters such as contrast sensitivity or mean defect and pattern standard deviation of the visual fields of some visual pathways. Our study shows that the magnocellular and koniocellular pathways are the most affected, so that these patients have impairment in motion perception and blue-yellow contrast perception. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

User-centered evaluation of Arizona BioPathway: an information extraction, integration, and visualization system.

PubMed

Quiñones, Karin D; Su, Hua; Marshall, Byron; Eggers, Shauna; Chen, Hsinchun

2007-09-01

Explosive growth in biomedical research has made automated information extraction, knowledge integration, and visualization increasingly important and critically needed. The Arizona BioPathway (ABP) system extracts and displays biological regulatory pathway information from the abstracts of journal articles. This study uses relations extracted from more than 200 PubMed abstracts presented in a tabular and graphical user interface with built-in search and aggregation functionality. This paper presents a task-centered assessment of the usefulness and usability of the ABP system focusing on its relation aggregation and visualization functionalities. Results suggest that our graph-based visualization is more efficient in supporting pathway analysis tasks and is perceived as more useful and easier to use as compared to a text-based literature-viewing method. Relation aggregation significantly contributes to knowledge-acquisition efficiency. Together, the graphic and tabular views in the ABP Visualizer provide a flexible and effective interface for pathway relation browsing and analysis. Our study contributes to pathway-related research and biological information extraction by assessing the value of a multiview, relation-based interface that supports user-controlled exploration of pathway information across multiple granularities.

In Vivo Evaluation of White Matter Integrity and Anterograde Transport in Visual System After Excitotoxic Retinal Injury With Multimodal MRI and OCT

PubMed Central

Ho, Leon C.; Wang, Bo; Conner, Ian P.; van der Merwe, Yolandi; Bilonick, Richard A.; Kim, Seong-Gi; Wu, Ed X.; Sigal, Ian A.; Wollstein, Gadi; Schuman, Joel S.; Chan, Kevin C.

2015-01-01

Purpose. Excitotoxicity has been linked to the pathogenesis of ocular diseases and injuries and may involve early degeneration of both anterior and posterior visual pathways. However, their spatiotemporal relationships remain unclear. We hypothesized that the effects of excitotoxic retinal injury (ERI) on the visual system can be revealed in vivo by diffusion tensor magnetic resonance imagining (DTI), manganese-enhanced magnetic resonance imagining (MRI), and optical coherence tomography (OCT). Methods. Diffusion tensor MRI was performed at 9.4 Tesla to monitor white matter integrity changes after unilateral N-methyl-D-aspartate (NMDA)-induced ERI in six Sprague-Dawley rats and six C57BL/6J mice. Additionally, four rats and four mice were intravitreally injected with saline to compare with NMDA-injected animals. Optical coherence tomography of the retina and manganese-enhanced MRI of anterograde transport were evaluated and correlated with DTI parameters. Results. In the rat optic nerve, the largest axial diffusivity decrease and radial diffusivity increase occurred within the first 3 and 7 days post ERI, respectively, suggestive of early axonal degeneration and delayed demyelination. The optic tract showed smaller directional diffusivity changes and weaker DTI correlations with retinal thickness compared with optic nerve, indicative of anterograde degeneration. The splenium of corpus callosum was also reorganized at 4 weeks post ERI. The DTI profiles appeared comparable between rat and mouse models. Furthermore, the NMDA-injured visual pathway showed reduced anterograde manganese transport, which correlated with diffusivity changes along but not perpendicular to optic nerve. Conclusions. Diffusion tensor MRI, manganese-enhanced MRI, and OCT provided an in vivo model system for characterizing the spatiotemporal changes in white matter integrity, the eye–brain relationships and structural–physiological relationships in the visual system after ERI. PMID:26066747

The ventral visual pathway: an expanded neural framework for the processing of object quality.

PubMed

Kravitz, Dwight J; Saleem, Kadharbatcha S; Baker, Chris I; Ungerleider, Leslie G; Mishkin, Mortimer

2013-01-01

Since the original characterization of the ventral visual pathway, our knowledge of its neuroanatomy, functional properties, and extrinsic targets has grown considerably. Here we synthesize this recent evidence and propose that the ventral pathway is best understood as a recurrent occipitotemporal network containing neural representations of object quality both utilized and constrained by at least six distinct cortical and subcortical systems. Each system serves its own specialized behavioral, cognitive, or affective function, collectively providing the raison d'être for the ventral visual pathway. This expanded framework contrasts with the depiction of the ventral visual pathway as a largely serial staged hierarchy culminating in singular object representations and more parsimoniously incorporates attentional, contextual, and feedback effects. Published by Elsevier Ltd.

The magnocellular visual pathway and facial emotion misattribution errors in schizophrenia.

PubMed

Bedwell, Jeffrey S; Chan, Chi C; Cohen, Ovad; Karbi, Yinnon; Shamir, Eyal; Rassovsky, Yuri

2013-07-01

Many individuals with schizophrenia show impairment in labeling the emotion depicted by faces, and tend to ascribe anger or fear to neutral expressions. Preliminary research has linked some of these difficulties to dysfunction in the magnocellular (M) visual pathway, which has direct projections to subcortical emotion processing regions. The current study attempted to clarify these relationships using a novel paradigm that included a red background. Diffuse red light is known to suppress the M-pathway in nonpsychiatric adults, and there is preliminary evidence that it may have the opposite (stimulating) effect in schizophrenia-spectrum disorders (SSDs). Twenty-five individuals with SSDs were compared with 31 nonpsychiatric controls using a facial emotion identification task depicting happy, angry, fearful, and sad emotions on red, green, and gray backgrounds. There was a robust interaction of group by change in errors to the red (vs. green) background for misattributing fear expressions as depicting anger (p=.001, ή(2)=.18). Specifically, controls showed a significant decrease in this type of error with the red background (p=.003, d=0.77), while the SSD group tended to increase this type of error (p=.07, d=0.54). These findings suggest that the well-established M-pathway abnormalities in SSDs may contribute to the heightened misperception of other emotions such as anger, which in turn may cause social misperceptions in the environment and elicit symptoms such as paranoia and social withdrawal. As the ventral striatum plays a primary role in identifying anger and receives efferent input from the M-pathway, it may serve as the neuroanatomical substrate in the perception of anger. Copyright © 2013 Elsevier Inc. All rights reserved.

Multiple Causal Links Between Magnocellular-Dorsal Pathway Deficit and Developmental Dyslexia.

PubMed

Gori, Simone; Seitz, Aaron R; Ronconi, Luca; Franceschini, Sandro; Facoetti, Andrea

2016-10-17

Although impaired auditory-phonological processing is the most popular explanation of developmental dyslexia (DD), the literature shows that the combination of several causes rather than a single factor contributes to DD. Functioning of the visual magnocellular-dorsal (MD) pathway, which plays a key role in motion perception, is a much debated, but heavily suspected factor contributing to DD. Here, we employ a comprehensive approach that incorporates all the accepted methods required to test the relationship between the MD pathway dysfunction and DD. The results of 4 experiments show that (1) Motion perception is impaired in children with dyslexia in comparison both with age-match and with reading-level controls; (2) pre-reading visual motion perception-independently from auditory-phonological skill-predicts future reading development, and (3) targeted MD trainings-not involving any auditory-phonological stimulation-leads to improved reading skill in children and adults with DD. Our findings demonstrate, for the first time, a causal relationship between MD deficits and DD, virtually closing a 30-year long debate. Since MD dysfunction can be diagnosed much earlier than reading and language disorders, our findings pave the way for low resource-intensive, early prevention programs that could drastically reduce the incidence of DD. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The human visual cortex responds to gene therapy–mediated recovery of retinal function

PubMed Central

Ashtari, Manzar; Cyckowski, Laura L.; Monroe, Justin F.; Marshall, Kathleen A.; Chung, Daniel C.; Auricchio, Alberto; Simonelli, Francesca; Leroy, Bart P.; Maguire, Albert M.; Shindler, Kenneth S.; Bennett, Jean

2011-01-01

Leber congenital amaurosis (LCA) is a rare degenerative eye disease, linked to mutations in at least 14 genes. A recent gene therapy trial in patients with LCA2, who have mutations in RPE65, demonstrated that subretinal injection of an adeno-associated virus (AAV) carrying the normal cDNA of that gene (AAV2-hRPE65v2) could markedly improve vision. However, it remains unclear how the visual cortex responds to recovery of retinal function after prolonged sensory deprivation. Here, 3 of the gene therapy trial subjects, treated at ages 8, 9, and 35 years, underwent functional MRI within 2 years of unilateral injection of AAV2-hRPE65v2. All subjects showed increased cortical activation in response to high- and medium-contrast stimuli after exposure to the treated compared with the untreated eye. Furthermore, we observed a correlation between the visual field maps and the distribution of cortical activations for the treated eyes. These data suggest that despite severe and long-term visual impairment, treated LCA2 patients have intact and responsive visual pathways. In addition, these data suggest that gene therapy resulted in not only sustained and improved visual ability, but also enhanced contrast sensitivity. PMID:21606598

Visual Contrast Sensitivity Improvement by Right Frontal High-Beta Activity Is Mediated by Contrast Gain Mechanisms and Influenced by Fronto-Parietal White Matter Microstructure

PubMed Central

Quentin, Romain; Elkin Frankston, Seth; Vernet, Marine; Toba, Monica N.; Bartolomeo, Paolo; Chanes, Lorena; Valero-Cabré, Antoni

2016-01-01

Behavioral and electrophysiological studies in humans and non-human primates have correlated frontal high-beta activity with the orienting of endogenous attention and shown the ability of the latter function to modulate visual performance. We here combined rhythmic transcranial magnetic stimulation (TMS) and diffusion imaging to study the relation between frontal oscillatory activity and visual performance, and we associated these phenomena to a specific set of white matter pathways that in humans subtend attentional processes. High-beta rhythmic activity on the right frontal eye field (FEF) was induced with TMS and its causal effects on a contrast sensitivity function were recorded to explore its ability to improve visual detection performance across different stimulus contrast levels. Our results show that frequency-specific activity patterns engaged in the right FEF have the ability to induce a leftward shift of the psychometric function. This increase in visual performance across different levels of stimulus contrast is likely mediated by a contrast gain mechanism. Interestingly, microstructural measures of white matter connectivity suggest a strong implication of right fronto-parietal connectivity linking the FEF and the intraparietal sulcus in propagating high-beta rhythmic signals across brain networks and subtending top-down frontal influences on visual performance. PMID:25899709

C. elegans Vulva Induction: An In Vivo Model to Study Epidermal Growth Factor Receptor Signaling and Trafficking.

PubMed

Gauthier, Kimberley; Rocheleau, Christian E

2017-01-01

Epidermal growth factor receptor (EGFR)-mediated activation of the canonical Ras/MAPK signaling cascade is responsible for cell proliferation and cell growth. This signaling pathway is frequently overactivated in epithelial cancers; therefore, studying regulation of this pathway is crucial not only for our fundamental understanding of cell biology but also for our ability to treat EGFR-related disease. Genetic model organisms such as Caenorhabditis elegans, a hermaphroditic nematode, played a vital role in identifying components of the EGFR/Ras/MAPK pathway and delineating their order of function, and continues to play a role in identifying novel regulators of the pathway. Polarized activation of LET-23, the C. elegans homolog of EGFR, is responsible for induction of the vulval cell fate; perturbations in this signaling pathway produce either a vulvaless or multivulva phenotype. The translucent cuticle of the nematode facilitates in vivo visualization of the receptor, revealing that localization of LET-23 EGFR is tightly regulated and linked to its function. In this chapter, we review the methods used to harness vulva development as a tool for studying EGFR signaling and trafficking in C. elegans.

The ventral visual pathway: An expanded neural framework for the processing of object quality

PubMed Central

Kravitz, Dwight J.; Saleem, Kadharbatcha S.; Baker, Chris I.; Ungerleider, Leslie G.; Mishkin, Mortimer

2012-01-01

Since the original characterization of the ventral visual pathway our knowledge of its neuroanatomy, functional properties, and extrinsic targets has grown considerably. Here we synthesize this recent evidence and propose that the ventral pathway is best understood as a recurrent occipitotemporal network containing neural representations of object quality both utilized and constrained by at least six distinct cortical and subcortical systems. Each system serves its own specialized behavioral, cognitive, or affective function, collectively providing the raison d’etre for the ventral visual pathway. This expanded framework contrasts with the depiction of the ventral visual pathway as a largely serial staged hierarchy that culminates in singular object representations for utilization mainly by ventrolateral prefrontal cortex and, more parsimoniously than this account, incorporates attentional, contextual, and feedback effects. PMID:23265839

Fine-grained temporal coding of visually-similar categories in the ventral visual pathway and prefrontal cortex

PubMed Central

Xu, Yang; D'Lauro, Christopher; Pyles, John A.; Kass, Robert E.; Tarr, Michael J.

2013-01-01

Humans are remarkably proficient at categorizing visually-similar objects. To better understand the cortical basis of this categorization process, we used magnetoencephalography (MEG) to record neural activity while participants learned–with feedback–to discriminate two highly-similar, novel visual categories. We hypothesized that although prefrontal regions would mediate early category learning, this role would diminish with increasing category familiarity and that regions within the ventral visual pathway would come to play a more prominent role in encoding category-relevant information as learning progressed. Early in learning we observed some degree of categorical discriminability and predictability in both prefrontal cortex and the ventral visual pathway. Predictability improved significantly above chance in the ventral visual pathway over the course of learning with the left inferior temporal and fusiform gyri showing the greatest improvement in predictability between 150 and 250 ms (M200) during category learning. In contrast, there was no comparable increase in discriminability in prefrontal cortex with the only significant post-learning effect being a decrease in predictability in the inferior frontal gyrus between 250 and 350 ms (M300). Thus, the ventral visual pathway appears to encode learned visual categories over the long term. At the same time these results add to our understanding of the cortical origins of previously reported signature temporal components associated with perceptual learning. PMID:24146656

Compromised Integrity of Central Visual Pathways in Patients With Macular Degeneration.

PubMed

Malania, Maka; Konrad, Julia; Jägle, Herbert; Werner, John S; Greenlee, Mark W

2017-06-01

Macular degeneration (MD) affects the central retina and leads to gradual loss of foveal vision. Although, photoreceptors are primarily affected in MD, the retinal nerve fiber layer (RNFL) and central visual pathways may also be altered subsequent to photoreceptor degeneration. Here we investigate whether retinal damage caused by MD alters microstructural properties of visual pathways using diffusion-weighted magnetic resonance imaging. Six MD patients and six healthy control subjects participated in the study. Retinal images were obtained by spectral-domain optical coherence tomography (SD-OCT). Diffusion tensor images (DTI) and high-resolution T1-weighted structural images were collected for each subject. We used diffusion-based tensor modeling and probabilistic fiber tractography to identify the optic tract (OT) and optic radiations (OR), as well as nonvisual pathways (corticospinal tract and anterior fibers of corpus callosum). Fractional anisotropy (FA) and axial and radial diffusivity values (AD, RD) were calculated along the nonvisual and visual pathways. Measurement of RNFL thickness reveals that the temporal circumpapillary retinal nerve fiber layer was significantly thinner in eyes with macular degeneration than normal. While we did not find significant differences in diffusion properties in nonvisual pathways, patients showed significant changes in diffusion scalars (FA, RD, and AD) both in OT and OR. The results indicate that the RNFL and the white matter of the visual pathways are significantly altered in MD patients. Damage to the photoreceptors in MD leads to atrophy of the ganglion cell axons and to corresponding changes in microstructural properties of central visual pathways.

A multi-pathway hypothesis for human visual fear signaling

PubMed Central

Silverstein, David N.; Ingvar, Martin

2015-01-01

A hypothesis is proposed for five visual fear signaling pathways in humans, based on an analysis of anatomical connectivity from primate studies and human functional connectvity and tractography from brain imaging studies. Earlier work has identified possible subcortical and cortical fear pathways known as the “low road” and “high road,” which arrive at the amygdala independently. In addition to a subcortical pathway, we propose four cortical signaling pathways in humans along the visual ventral stream. All four of these traverse through the LGN to the visual cortex (VC) and branching off at the inferior temporal area, with one projection directly to the amygdala; another traversing the orbitofrontal cortex; and two others passing through the parietal and then prefrontal cortex, one excitatory pathway via the ventral-medial area and one regulatory pathway via the ventral-lateral area. These pathways have progressively longer propagation latencies and may have progressively evolved with brain development to take advantage of higher-level processing. Using the anatomical path lengths and latency estimates for each of these five pathways, predictions are made for the relative processing times at selective ROIs and arrival at the amygdala, based on the presentation of a fear-relevant visual stimulus. Partial verification of the temporal dynamics of this hypothesis might be accomplished using experimental MEG analysis. Possible experimental protocols are suggested. PMID:26379513

Parallel pathways for cross-modal memory retrieval in Drosophila.

PubMed

Zhang, Xiaonan; Ren, Qingzhong; Guo, Aike

2013-05-15

Memory-retrieval processing of cross-modal sensory preconditioning is vital for understanding the plasticity underlying the interactions between modalities. As part of the sensory preconditioning paradigm, it has been hypothesized that the conditioned response to an unreinforced cue depends on the memory of the reinforced cue via a sensory link between the two cues. To test this hypothesis, we studied cross-modal memory-retrieval processing in a genetically tractable model organism, Drosophila melanogaster. By expressing the dominant temperature-sensitive shibire(ts1) (shi(ts1)) transgene, which blocks synaptic vesicle recycling of specific neural subsets with the Gal4/UAS system at the restrictive temperature, we specifically blocked visual and olfactory memory retrieval, either alone or in combination; memory acquisition remained intact for these modalities. Blocking the memory retrieval of the reinforced olfactory cues did not impair the conditioned response to the unreinforced visual cues or vice versa, in contrast to the canonical memory-retrieval processing of sensory preconditioning. In addition, these conditioned responses can be abolished by blocking the memory retrieval of the two modalities simultaneously. In sum, our results indicated that a conditioned response to an unreinforced cue in cross-modal sensory preconditioning can be recalled through parallel pathways.

Biocharts: a visual formalism for complex biological systems

PubMed Central

Kugler, Hillel; Larjo, Antti; Harel, David

2010-01-01

We address one of the central issues in devising languages, methods and tools for the modelling and analysis of complex biological systems, that of linking high-level (e.g. intercellular) information with lower-level (e.g. intracellular) information. Adequate ways of dealing with this issue are crucial for understanding biological networks and pathways, which typically contain huge amounts of data that continue to grow as our knowledge and understanding of a system increases. Trying to comprehend such data using the standard methods currently in use is often virtually impossible. We propose a two-tier compound visual language, which we call Biocharts, that is geared towards building fully executable models of biological systems. One of the main goals of our approach is to enable biologists to actively participate in the computational modelling effort, in a natural way. The high-level part of our language is a version of statecharts, which have been shown to be extremely successful in software and systems engineering. The statecharts can be combined with any appropriately well-defined language (preferably a diagrammatic one) for specifying the low-level dynamics of the pathways and networks. We illustrate the language and our general modelling approach using the well-studied process of bacterial chemotaxis. PMID:20022895

LinkedOmics: analyzing multi-omics data within and across 32 cancer types.

PubMed

Vasaikar, Suhas V; Straub, Peter; Wang, Jing; Zhang, Bing

2018-01-04

The LinkedOmics database contains multi-omics data and clinical data for 32 cancer types and a total of 11 158 patients from The Cancer Genome Atlas (TCGA) project. It is also the first multi-omics database that integrates mass spectrometry (MS)-based global proteomics data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) on selected TCGA tumor samples. In total, LinkedOmics has more than a billion data points. To allow comprehensive analysis of these data, we developed three analysis modules in the LinkedOmics web application. The LinkFinder module allows flexible exploration of associations between a molecular or clinical attribute of interest and all other attributes, providing the opportunity to analyze and visualize associations between billions of attribute pairs for each cancer cohort. The LinkCompare module enables easy comparison of the associations identified by LinkFinder, which is particularly useful in multi-omics and pan-cancer analyses. The LinkInterpreter module transforms identified associations into biological understanding through pathway and network analysis. Using five case studies, we demonstrate that LinkedOmics provides a unique platform for biologists and clinicians to access, analyze and compare cancer multi-omics data within and across tumor types. LinkedOmics is freely available at http://www.linkedomics.org. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Effects of visual attention on chromatic and achromatic detection sensitivities.

PubMed

Uchikawa, Keiji; Sato, Masayuki; Kuwamura, Keiko

2014-05-01

Visual attention has a significant effect on various visual functions, such as response time, detection and discrimination sensitivity, and color appearance. It has been suggested that visual attention may affect visual functions in the early visual pathways. In this study we examined selective effects of visual attention on sensitivities of the chromatic and achromatic pathways to clarify whether visual attention modifies responses in the early visual system. We used a dual task paradigm in which the observer detected a peripheral test stimulus presented at 4 deg eccentricities while the observer concurrently carried out an attention task in the central visual field. In experiment 1, it was confirmed that peripheral spectral sensitivities were reduced more for short and long wavelengths than for middle wavelengths with the central attention task so that the spectral sensitivity function changed its shape by visual attention. This indicated that visual attention affected the chromatic response more strongly than the achromatic response. In experiment 2 it was obtained that the detection thresholds increased in greater degrees in the red-green and yellow-blue chromatic directions than in the white-black achromatic direction in the dual task condition. In experiment 3 we showed that the peripheral threshold elevations depended on the combination of color-directions of the central and peripheral stimuli. Since the chromatic and achromatic responses were separately processed in the early visual pathways, the present results provided additional evidence that visual attention affects responses in the early visual pathways.

Organization of area hV5/MT+ in subjects with homonymous visual field defects.

PubMed

Papanikolaou, Amalia; Keliris, Georgios A; Papageorgiou, T Dorina; Schiefer, Ulrich; Logothetis, Nikos K; Smirnakis, Stelios M

2018-04-06

Damage to the primary visual cortex (V1) leads to a visual field loss (scotoma) in the retinotopically corresponding part of the visual field. Nonetheless, a small amount of residual visual sensitivity persists within the blind field. This residual capacity has been linked to activity observed in the middle temporal area complex (V5/MT+). However, it remains unknown whether the organization of hV5/MT+ changes following early visual cortical lesions. We studied the organization of area hV5/MT+ of five patients with dense homonymous defects in a quadrant of the visual field as a result of partial V1+ or optic radiation lesions. To do so, we developed a new method, which models the boundaries of population receptive fields directly from the BOLD signal of each voxel in the visual cortex. We found responses in hV5/MT+ arising inside the scotoma for all patients and identified two possible sources of activation: 1) responses might originate from partially lesioned parts of area V1 corresponding to the scotoma, and 2) responses can also originate independent of area V1 input suggesting the existence of functional V1-bypassing pathways. Apparently, visually driven activity observed in hV5/MT+ is not sufficient to mediate conscious vision. More surprisingly, visually driven activity in corresponding regions of V1 and early extrastriate areas including hV5/MT+ did not guarantee visual perception in the group of patients with post-geniculate lesions that we examined. This suggests that the fine coordination of visual activity patterns across visual areas may be an important determinant of whether visual perception persists following visual cortical lesions. Copyright © 2018 Elsevier Inc. All rights reserved.

Time-Resolved Proteomic Visualization of Dendrimer Cellular Entry and Trafficking.

PubMed

Wang, Linna; Yang, Li; Pan, Li; Kadasala, Naveen Reddy; Xue, Liang; Schuster, Robert J; Parker, Laurie L; Wei, Alexander; Tao, W Andy

2015-10-14

Our understanding of the complex cell entry pathways would greatly benefit from a comprehensive characterization of key proteins involved in this dynamic process. Here we devise a novel proteomic strategy named TITAN (Tracing Internalization and TrAfficking of Nanomaterials) to reveal real-time protein-dendrimer interactions using a systems biology approach. Dendrimers functionalized with photoreactive cross-linkers were internalized by HeLa cells and irradiated at set time intervals, then isolated and subjected to quantitative proteomics. In total, 809 interacting proteins cross-linked with dendrimers were determined by TITAN in a detailed temporal manner during dendrimer internalization, traceable to at least two major endocytic mechanisms, clathrin-mediated and caveolar/raft-mediated endocytosis. The direct involvement of the two pathways was further established by the inhibitory effect of dynasore on dendrimer uptake and changes in temporal profiles of key proteins.

AMD and the alternative complement pathway: genetics and functional implications.

PubMed

Tan, Perciliz L; Bowes Rickman, Catherine; Katsanis, Nicholas

2016-06-21

Age-related macular degeneration (AMD) is an ocular neurodegenerative disorder and is the leading cause of legal blindness in Western societies, with a prevalence of up to 8 % over the age of 60, which continues to increase with age. AMD is characterized by the progressive breakdown of the macula (the central region of the retina), resulting in the loss of central vision including visual acuity. While its molecular etiology remains unclear, advances in genetics and genomics have illuminated the genetic architecture of the disease and have generated attractive pathomechanistic hypotheses. Here, we review the genetic architecture of AMD, considering the contribution of both common and rare alleles to susceptibility, and we explore the possible mechanistic links between photoreceptor degeneration and the alternative complement pathway, a cascade that has emerged as the most potent genetic driver of this disorder.

Delayed Early Primary Visual Pathway Development in Premature Infants: High Density Electrophysiological Evidence

PubMed Central

Tremblay, Emmanuel; Vannasing, Phetsamone; Roy, Marie-Sylvie; Lefebvre, Francine; Kombate, Damelan; Lassonde, Maryse; Lepore, Franco; McKerral, Michelle; Gallagher, Anne

2014-01-01

In the past decades, multiple studies have been interested in developmental patterns of the visual system in healthy infants. During the first year of life, differential maturational changes have been observed between the Magnocellular (P) and the Parvocellular (P) visual pathways. However, few studies investigated P and M system development in infants born prematurely. The aim of the present study was to characterize P and M system maturational differences between healthy preterm and fullterm infants through a critical period of visual maturation: the first year of life. Using a cross-sectional design, high-density electroencephalogram (EEG) was recorded in 31 healthy preterms and 41 fullterm infants of 3, 6, or 12 months (corrected age for premature babies). Three visual stimulations varying in contrast and spatial frequency were presented to stimulate preferentially the M pathway, the P pathway, or both systems simultaneously during EEG recordings. Results from early visual evoked potentials in response to the stimulation that activates simultaneously both systems revealed longer N1 latencies and smaller P1 amplitudes in preterm infants compared to fullterms. Moreover, preterms showed longer N1 and P1 latencies in response to stimuli assessing the M pathway at 3 months. No differences between preterms and fullterms were found when using the preferential P system stimulation. In order to identify the cerebral generator of each visual response, distributed source analyses were computed in 12-month-old infants using LORETA. Source analysis demonstrated an activation of the parietal dorsal region in fullterm infants, in response to the preferential M pathway, which was not seen in the preterms. Overall, these findings suggest that the Magnocellular pathway development is affected in premature infants. Although our VEP results suggest that premature children overcome, at least partially, the visual developmental delay with time, source analyses reveal abnormal brain activation of the Magnocellular pathway at 12 months of age. PMID:25268226

More than blindsight: Case report of a child with extraordinary visual capacity following perinatal bilateral occipital lobe injury.

PubMed

Mundinano, Inaki-Carril; Chen, Juan; de Souza, Mitchell; Sarossy, Marc G; Joanisse, Marc F; Goodale, Melvyn A; Bourne, James A

2017-11-13

Injury to the primary visual cortex (V1, striate cortex) and the geniculostriate pathway in adults results in cortical blindness, abolishing conscious visual perception. Early studies by Larry Weiskrantz and colleagues demonstrated that some patients with an occipital-lobe injury exhibited a degree of unconscious vision and visually-guided behaviour within the blind field. A more recent focus has been the observed phenomenon whereby early-life injury to V1 often results in the preservation of visual perception in both monkeys and humans. These findings initiated a concerted effort on multiple fronts, including nonhuman primate studies, to uncover the neural substrate/s of the spared conscious vision. In both adult and early-life cases of V1 injury, evidence suggests the involvement of the Middle Temporal area (MT) of the extrastriate visual cortex, which is an integral component area of the dorsal stream and is also associated with visually-guided behaviors. Because of the limited number of early-life V1 injury cases for humans, the outstanding question in the field is what secondary visual pathways are responsible for this extraordinary capacity? Here we report for the first time a case of a child (B.I.) who suffered a bilateral occipital-lobe injury in the first two weeks postnatally due to medium-chain acyl-Co-A dehydrogenase deficiency. At 6 years of age, B.I. underwent a battery of neurophysiological tests, as well as structural and diffusion MRI and ophthalmic examination at 7 years. Despite the extensive bilateral occipital cortical damage, B.I. has extensive conscious visual abilities, is not blind, and can use vision to navigate his environment. Furthermore, unlike blindsight patients, he can readily and consciously identify happy and neutral faces and colors, tasks associated with ventral stream processing. These findings suggest significant re-routing of visual information. To identify the putative visual pathway/s responsible for this ability, MRI tractography of secondary visual pathways connecting MT with the lateral geniculate nucleus (LGN) and the inferior pulvinar (PI) were analysed. Results revealed an increased PI-MT pathway in the left hemisphere, suggesting that this pulvinar relay could be the neural pathway affording the preserved visual capacity following an early-life lesion of V1. These findings corroborate anatomical evidence from monkeys showing an enhanced PI-MT pathway following an early-life lesion of V1, compared to adults. Copyright © 2017 Elsevier Ltd. All rights reserved.

The role of human ventral visual cortex in motion perception

PubMed Central

Saygin, Ayse P.; Lorenzi, Lauren J.; Egan, Ryan; Rees, Geraint; Behrmann, Marlene

2013-01-01

Visual motion perception is fundamental to many aspects of visual perception. Visual motion perception has long been associated with the dorsal (parietal) pathway and the involvement of the ventral ‘form’ (temporal) visual pathway has not been considered critical for normal motion perception. Here, we evaluated this view by examining whether circumscribed damage to ventral visual cortex impaired motion perception. The perception of motion in basic, non-form tasks (motion coherence and motion detection) and complex structure-from-motion, for a wide range of motion speeds, all centrally displayed, was assessed in five patients with a circumscribed lesion to either the right or left ventral visual pathway. Patients with a right, but not with a left, ventral visual lesion displayed widespread impairments in central motion perception even for non-form motion, for both slow and for fast speeds, and this held true independent of the integrity of areas MT/V5, V3A or parietal regions. In contrast with the traditional view in which only the dorsal visual stream is critical for motion perception, these novel findings implicate a more distributed circuit in which the integrity of the right ventral visual pathway is also necessary even for the perception of non-form motion. PMID:23983030

Resilience to the contralateral visual field bias as a window into object representations

PubMed Central

Garcea, Frank E.; Kristensen, Stephanie; Almeida, Jorge; Mahon, Bradford Z.

2016-01-01

Viewing images of manipulable objects elicits differential blood oxygen level-dependent (BOLD) contrast across parietal and dorsal occipital areas of the human brain that support object-directed reaching, grasping, and complex object manipulation. However, it is unknown which object-selective regions of parietal cortex receive their principal inputs from the ventral object-processing pathway and which receive their inputs from the dorsal object-processing pathway. Parietal areas that receive their inputs from the ventral visual pathway, rather than from the dorsal stream, will have inputs that are already filtered through object categorization and identification processes. This predicts that parietal regions that receive inputs from the ventral visual pathway should exhibit object-selective responses that are resilient to contralateral visual field biases. To test this hypothesis, adult participants viewed images of tools and animals that were presented to the left or right visual fields during functional magnetic resonance imaging (fMRI). We found that the left inferior parietal lobule showed robust tool preferences independently of the visual field in which tool stimuli were presented. In contrast, a region in posterior parietal/dorsal occipital cortex in the right hemisphere exhibited an interaction between visual field and category: tool-preferences were strongest contralateral to the stimulus. These findings suggest that action knowledge accessed in the left inferior parietal lobule operates over inputs that are abstracted from the visual input and contingent on analysis by the ventral visual pathway, consistent with its putative role in supporting object manipulation knowledge. PMID:27160998

Emergence of Orientation Selectivity in the Mammalian Visual Pathway

PubMed Central

Scholl, Benjamin; Tan, Andrew Y. Y.; Corey, Joseph

2013-01-01

Orientation selectivity is a property of mammalian primary visual cortex (V1) neurons, yet its emergence along the visual pathway varies across species. In carnivores and primates, elongated receptive fields first appear in V1, whereas in lagomorphs such receptive fields emerge earlier, in the retina. Here we examine the mouse visual pathway and reveal the existence of orientation selectivity in lateral geniculate nucleus (LGN) relay cells. Cortical inactivation does not reduce this orientation selectivity, indicating that cortical feedback is not its source. Orientation selectivity is similar for LGN relay cells spiking and subthreshold input to V1 neurons, suggesting that cortical orientation selectivity is inherited from the LGN in mouse. In contrast, orientation selectivity of cat LGN relay cells is small relative to subthreshold inputs onto V1 simple cells. Together, these differences show that although orientation selectivity exists in visual neurons of both rodents and carnivores, its emergence along the visual pathway, and thus its underlying neuronal circuitry, is fundamentally different. PMID:23804085

SPV: a JavaScript Signaling Pathway Visualizer.

PubMed

Calderone, Alberto; Cesareni, Gianni

2018-03-24

The visualization of molecular interactions annotated in web resources is useful to offer to users such information in a clear intuitive layout. These interactions are frequently represented as binary interactions that are laid out in free space where, different entities, cellular compartments and interaction types are hardly distinguishable. SPV (Signaling Pathway Visualizer) is a free open source JavaScript library which offers a series of pre-defined elements, compartments and interaction types meant to facilitate the representation of signaling pathways consisting of causal interactions without neglecting simple protein-protein interaction networks. freely available under Apache version 2 license; Source code: https://github.com/Sinnefa/SPV_Signaling_Pathway_Visualizer_v1.0. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js. sinnefa@gmail.com.

Visual Outcomes in Pediatric Optic Pathway Glioma After Conformal Radiation Therapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Awdeh, Richard M.; Kiehna, Erin N.; Drewry, Richard D.

Purpose: To assess visual outcome prospectively after conformal radiation therapy (CRT) in children with optic pathway glioma. Methods and Materials: We used CRT to treat optic pathway glioma in 20 children (median age 9.3 years) between July 1997 and January 2002. We assessed changes in visual acuity using the logarithm of the minimal angle of resolution after CRT (54 Gy) with a median follow-up of 24 months. We included in the study children who underwent chemotherapy (8 patients) or resection (9 patients) before CRT. Results: Surgery played a major role in determining baseline (pre-CRT) visual acuity (better eye: P=.0431; worsemore » eye: P=.0032). The visual acuity in the worse eye was diminished at baseline (borderline significant) with administration of chemotherapy before CRT (P=.0726) and progression of disease prior to receiving CRT (P=.0220). In the worse eye, improvement in visual acuity was observed in patients who did not receive chemotherapy before CRT (P=.0289). Conclusions: Children with optic pathway glioma initially treated with chemotherapy prior to receiving radiation therapy have decreased visual acuity compared with those who receive primary radiation therapy. Limited surgery before radiation therapy may have a role in preserving visual acuity.« less

A taxonomy of visualization tasks for the analysis of biological pathway data.

PubMed

Murray, Paul; McGee, Fintan; Forbes, Angus G

2017-02-15

Understanding complicated networks of interactions and chemical components is essential to solving contemporary problems in modern biology, especially in domains such as cancer and systems research. In these domains, biological pathway data is used to represent chains of interactions that occur within a given biological process. Visual representations can help researchers understand, interact with, and reason about these complex pathways in a number of ways. At the same time, these datasets offer unique challenges for visualization, due to their complexity and heterogeneity. Here, we present taxonomy of tasks that are regularly performed by researchers who work with biological pathway data. The generation of these tasks was done in conjunction with interviews with several domain experts in biology. These tasks require further classification than is provided by existing taxonomies. We also examine existing visualization techniques that support each task, and we discuss gaps in the existing visualization space revealed by our taxonomy. Our taxonomy is designed to support the development and design of future biological pathway visualization applications. We conclude by suggesting future research directions based on our taxonomy and motivated by the comments received by our domain experts.

Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability

PubMed Central

Pathak, Rajesh Kumar; Gupta, Sanjay Mohan; Gaur, Vikram Singh; Pandey, Dinesh

2015-01-01

Abstract In recent years, rapid developments in several omics platforms and next generation sequencing technology have generated a huge amount of biological data about plants. Systems biology aims to develop and use well-organized and efficient algorithms, data structure, visualization, and communication tools for the integration of these biological data with the goal of computational modeling and simulation. It studies crop plant systems by systematically perturbing them, checking the gene, protein, and informational pathway responses; integrating these data; and finally, formulating mathematical models that describe the structure of system and its response to individual perturbations. Consequently, systems biology approaches, such as integrative and predictive ones, hold immense potential in understanding of molecular mechanism of agriculturally important complex traits linked to agricultural productivity. This has led to identification of some key genes and proteins involved in networks of pathways involved in input use efficiency, biotic and abiotic stress resistance, photosynthesis efficiency, root, stem and leaf architecture, and nutrient mobilization. The developments in the above fields have made it possible to design smart crops with superior agronomic traits through genetic manipulation of key candidate genes. PMID:26484978

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.

PubMed

Dogrusoz, U; Erson, E Z; Giral, E; Demir, E; Babur, O; Cetintas, A; Colak, R

2006-02-01

Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.

Visual agnosia and focal brain injury.

PubMed

Martinaud, O

Visual agnosia encompasses all disorders of visual recognition within a selective visual modality not due to an impairment of elementary visual processing or other cognitive deficit. Based on a sequential dichotomy between the perceptual and memory systems, two different categories of visual object agnosia are usually considered: 'apperceptive agnosia' and 'associative agnosia'. Impaired visual recognition within a single category of stimuli is also reported in: (i) visual object agnosia of the ventral pathway, such as prosopagnosia (for faces), pure alexia (for words), or topographagnosia (for landmarks); (ii) visual spatial agnosia of the dorsal pathway, such as cerebral akinetopsia (for movement), or orientation agnosia (for the placement of objects in space). Focal brain injuries provide a unique opportunity to better understand regional brain function, particularly with the use of effective statistical approaches such as voxel-based lesion-symptom mapping (VLSM). The aim of the present work was twofold: (i) to review the various agnosia categories according to the traditional visual dual-pathway model; and (ii) to better assess the anatomical network underlying visual recognition through lesion-mapping studies correlating neuroanatomical and clinical outcomes. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Electroretinography and Visual Evoked Potentials in Childhood Brain Tumor Survivors.

PubMed

Pietilä, Sari; Lenko, Hanna L; Oja, Sakari; Koivisto, Anna-Maija; Pietilä, Timo; Mäkipernaa, Anne

2016-07-01

This population-based cross-sectional study evaluates the clinical value of electroretinography and visual evoked potentials in childhood brain tumor survivors. A flash electroretinography and a checkerboard reversal pattern visual evoked potential (or alternatively a flash visual evoked potential) were done for 51 survivors (age 3.8-28.7 years) after a mean follow-up time of 7.6 (1.5-15.1) years. Abnormal electroretinography was obtained in 1 case, bilaterally delayed abnormal visual evoked potentials in 22/51 (43%) cases. Nine of 25 patients with infratentorial tumor location, and altogether 12 out of 31 (39%) patients who did not have tumors involving the visual pathways, had abnormal visual evoked potentials. Abnormal electroretinographies are rarely observed, but abnormal visual evoked potentials are common even without evident anatomic lesions in the visual pathway. Bilateral changes suggest a general and possibly multifactorial toxic/adverse effect on the visual pathway. Electroretinography and visual evoked potential may have clinical and scientific value while evaluating long-term effects of childhood brain tumors and tumor treatment. © The Author(s) 2016.

Multiple receptors coupled to phospholipase C gate long-term depression in visual cortex.

PubMed

Choi, Se-Young; Chang, Jeff; Jiang, Bin; Seol, Geun-Hee; Min, Sun-Seek; Han, Jung-Soo; Shin, Hee-Sup; Gallagher, Michela; Kirkwood, Alfredo

2005-12-07

Long-term depression (LTD) in sensory cortices depends on the activation of NMDA receptors. Here, we report that in visual cortical slices, the induction of LTD (but not long-term potentiation) also requires the activation of receptors coupled to the phospholipase C (PLC) pathway. Using immunolesions in combination with agonists and antagonists, we selectively manipulated the activation of alpha1 adrenergic, M1 muscarinic, and mGluR5 glutamatergic receptors. Inactivation of these PLC-coupled receptors prevents the induction of LTD, but only when the three receptors were inactivated together. LTD is fully restored by activating any one of them or by supplying intracellular D-myo-inositol-1,4,5-triphosphate (IP3). LTD was also impaired by intracellular application of PLC or IP3 receptor blockers, and it was absent in mice lacking PLCbeta1, the predominant PLC isoform in the forebrain. We propose that visual cortical LTD requires a minimum of PLC activity that can be supplied independently by at least three neurotransmitter systems. This essential requirement places PLC-linked receptors in a unique position to control the induction of LTD and provides a mechanism for gating visual cortical plasticity via extra-retinal inputs in the intact organism.

Visualization and Hierarchical Analysis of Flow in Discrete Fracture Network Models

NASA Astrophysics Data System (ADS)

Aldrich, G. A.; Gable, C. W.; Painter, S. L.; Makedonska, N.; Hamann, B.; Woodring, J.

2013-12-01

Flow and transport in low permeability fractured rock is primary in interconnected fracture networks. Prediction and characterization of flow and transport in fractured rock has important implications in underground repositories for hazardous materials (eg. nuclear and chemical waste), contaminant migration and remediation, groundwater resource management, and hydrocarbon extraction. We have developed methods to explicitly model flow in discrete fracture networks and track flow paths using passive particle tracking algorithms. Visualization and analysis of particle trajectory through the fracture network is important to understanding fracture connectivity, flow patterns, potential contaminant pathways and fast paths through the network. However, occlusion due to the large number of highly tessellated and intersecting fracture polygons preclude the effective use of traditional visualization methods. We would also like quantitative analysis methods to characterize the trajectory of a large number of particle paths. We have solved these problems by defining a hierarchal flow network representing the topology of particle flow through the fracture network. This approach allows us to analyses the flow and the dynamics of the system as a whole. We are able to easily query the flow network, and use paint-and-link style framework to filter the fracture geometry and particle traces based on the flow analytics. This allows us to greatly reduce occlusion while emphasizing salient features such as the principal transport pathways. Examples are shown that demonstrate the methodology and highlight how use of this new method allows quantitative analysis and characterization of flow and transport in a number of representative fracture networks.

Auditory and visual interhemispheric communication in musicians and non-musicians.

PubMed

Woelfle, Rebecca; Grahn, Jessica A

2013-01-01

The corpus callosum (CC) is a brain structure composed of axon fibres linking the right and left hemispheres. Musical training is associated with larger midsagittal cross-sectional area of the CC, suggesting that interhemispheric communication may be faster in musicians. Here we compared interhemispheric transmission times (ITTs) for musicians and non-musicians. ITT was measured by comparing simple reaction times to stimuli presented to the same hemisphere that controlled a button-press response (uncrossed reaction time), or to the contralateral hemisphere (crossed reaction time). Both visual and auditory stimuli were tested. We predicted that the crossed-uncrossed difference (CUD) for musicians would be smaller than for non-musicians as a result of faster interhemispheric transfer times. We did not expect a difference in CUDs between the visual and auditory modalities for either musicians or non-musicians, as previous work indicates that interhemispheric transfer may happen through the genu of the CC, which contains motor fibres rather than sensory fibres. There were no significant differences in CUDs between musicians and non-musicians. However, auditory CUDs were significantly smaller than visual CUDs. Although this auditory-visual difference was larger in musicians than non-musicians, the interaction between modality and musical training was not significant. Therefore, although musical training does not significantly affect ITT, the crossing of auditory information between hemispheres appears to be faster than visual information, perhaps because subcortical pathways play a greater role for auditory interhemispheric transfer.

Visual-vestibular processing deficits in mild traumatic brain injury.

PubMed

Wright, W G; Tierney, R T; McDevitt, J

2017-01-01

The search for reliable and valid signs and symptoms of mild traumatic brain injury (mTBI), commonly synonymous with concussion, has lead to a growing body of evidence that individuals with long-lasting, unremitting impairments often experience visual and vestibular symptoms, such as dizziness, postural and gait disturbances. Investigate the role of visual-vestibular processing deficits following concussion. A number of clinically accepted vestibular, oculomotor, and balance assessments as well as a novel virtual reality (VR)-based balance assessment device were used to assess adults with post-acute concussion (n = 14) in comparison to a healthy age-matched cohort (n = 58). Significant between-group differences were found with the VR-based balance device (p = 0.001), with dynamic visual motion emerging as the most discriminating balance condition. The symptom reports collected after performing the oculomotor and vestibular tests: rapid alternating horizontal eye saccades, optokinetic stimulation, and gaze stabilization, were all sensitive to health status (p < 0.05), despite the absence of oculomotor abnormalities being observed, except for near-point convergence. The BESS, King-Devick, and Dynamic Visual Acuity tests did not detect between-group differences. Postural and visual-vestibular tasks most closely linked to spatial and self-motion perception had the greatest discriminatory outcomes. The current findings suggest that mesencephalic and parieto-occipital centers and pathways may be involved in concussion.

Methane attenuates retinal ischemia/reperfusion injury via anti-oxidative and anti-apoptotic pathways.

PubMed

Liu, Lin; Sun, Qinglei; Wang, Ruobing; Chen, Zeli; Wu, Jiangchun; Xia, Fangzhou; Fan, Xian-Qun

2016-09-01

Retinal ischemia/reperfusion injury (IRI) may cause incurable visual impairment due to neural regeneration limits. Methane was shown to exert a protective effect against IRI in many organs. This study aims to explore the possible protective effects of methane-rich saline against retinal IRI in rat. Retinal IRI was performed on the right eyes of male Sprague-Dawley rats, which were immediately injected intraperitoneally with methane-saturated saline (25ml/kg). At one week after surgery, the number of retinal ganglion cells (RGCs), total retinal thickness, visual function were measured by hematoxylin and eosin staining, FluoroGold anterograde labeling and flash visual evoked potentials. The levels of 8-hydroxy-2-deoxyguanosine (8-OHdG), 4-Hydroxy-2-nonenal (4-HNE), malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx), caspase-3, caspase-9, B cell lymphoma/leukemia-2 (Bcl-2) and Bcl-2 associated X protein (Bax) in retinas were assessed by immunofluorescence staining, enzyme-linked immunosorbent assay and quantitative polymerase chain reaction. As expected, methane treatment significantly improved the retinal IRI-induced RGC loss, total retinal layer thinning and visual dysfunction. Moreover, methane treatment significantly reduced the levels of oxidative stress biomarkers (8-OHdG, 4-HNE, MDA) and increased the antioxidant enzyme activities (SOD, CAT, GPx) in the retinas with IRI. Meanwhile, methane treatment significantly increased the anti-apoptotic gene (Bcl-2) expression and decreased the pro-apoptotic gene (Bax) expression, accompanied by the suppression of caspase-3 and caspase-9 activity. Thus, these data demonstrated that methane can exert a neuroprotective role against retinal IRI through anti-oxidative and anti-apoptotic pathways. Copyright © 2016. Published by Elsevier B.V.

Feature-Specific Organization of Feedback Pathways in Mouse Visual Cortex.

PubMed

Huh, Carey Y L; Peach, John P; Bennett, Corbett; Vega, Roxana M; Hestrin, Shaul

2018-01-08

Higher and lower cortical areas in the visual hierarchy are reciprocally connected [1]. Although much is known about how feedforward pathways shape receptive field properties of visual neurons, relatively little is known about the role of feedback pathways in visual processing. Feedback pathways are thought to carry top-down signals, including information about context (e.g., figure-ground segmentation and surround suppression) [2-5], and feedback has been demonstrated to sharpen orientation tuning of neurons in the primary visual cortex (V1) [6, 7]. However, the response characteristics of feedback neurons themselves and how feedback shapes V1 neurons' tuning for other features, such as spatial frequency (SF), remain largely unknown. Here, using a retrograde virus, targeted electrophysiological recordings, and optogenetic manipulations, we show that putatively feedback neurons in layer 5 (hereafter "L5 feedback") in higher visual areas, AL (anterolateral area) and PM (posteromedial area), display distinct visual properties in awake head-fixed mice. AL L5 feedback neurons prefer significantly lower SF (mean: 0.04 cycles per degree [cpd]) compared to PM L5 feedback neurons (0.15 cpd). Importantly, silencing AL L5 feedback reduced visual responses of V1 neurons preferring low SF (mean change in firing rate: -8.0%), whereas silencing PM L5 feedback suppressed responses of high-SF-preferring V1 neurons (-20.4%). These findings suggest that feedback connections from higher visual areas convey distinctly tuned visual inputs to V1 that serve to boost V1 neurons' responses to SF. Such like-to-like functional organization may represent an important feature of feedback pathways in sensory systems and in the nervous system in general. Copyright © 2017 Elsevier Ltd. All rights reserved.

Neural Pathways Conveying Novisual Information to the Visual Cortex

PubMed Central

2013-01-01

The visual cortex has been traditionally considered as a stimulus-driven, unimodal system with a hierarchical organization. However, recent animal and human studies have shown that the visual cortex responds to non-visual stimuli, especially in individuals with visual deprivation congenitally, indicating the supramodal nature of the functional representation in the visual cortex. To understand the neural substrates of the cross-modal processing of the non-visual signals in the visual cortex, we firstly showed the supramodal nature of the visual cortex. We then reviewed how the nonvisual signals reach the visual cortex. Moreover, we discussed if these non-visual pathways are reshaped by early visual deprivation. Finally, the open question about the nature (stimulus-driven or top-down) of non-visual signals is also discussed. PMID:23840972

Elaboration of the Visual Pathways from the Study of War-Related Cranial Injuries: The Period from the Russo-Japanese War to World War I.

PubMed

Lanska, Douglas J

2016-01-01

As a result of the wars in the early 20th century, elaboration of the visual pathways was greatly facilitated by the meticulous study of visual defects in soldiers who had suffered focal injuries to the visual cortex. Using relatively crude techniques, often under difficult wartime circumstances, investigators successfully mapped key features of the visual pathways. Studies during the Russo- Japanese War (1904-1905) by Tatsuji Inouye (1881-1976) and during World War I by Gordon Holmes (1876-1965), William Lister (1868-1944), and others produced increasingly refined retinotopic maps of the primary visual cortex, which were later supported and refined by studies during and after World War II. Studies by George Riddoch (1888-1947) during World War I also demonstrated that some patients could still perceive motion despite blindness caused by damage to their visual cortex and helped to establish the concept of functional partitioning of visual processes in the occipital cortex. © 2016 S. Karger AG, Basel.

Biomarker-guided translation of brain imaging into disease pathway models

PubMed Central

Younesi, Erfan; Hofmann-Apitius, Martin

2013-01-01

The advent of state-of-the-art brain imaging technologies in recent years and the ability of such technologies to provide high-resolution information at both structural and functional levels has spawned large efforts to introduce novel non-invasive imaging biomarkers for early prediction and diagnosis of brain disorders; however, their utility in both clinic and drug development at their best resolution remains limited to visualizing and monitoring disease progression. Given the fact that efficient translation of valuable information embedded in brain scans into clinical application is of paramount scientific and public health importance, a strategy is needed to bridge the current gap between imaging and molecular biology, particularly in neurodegenerative diseases. As an attempt to address this issue, we present a novel computational method to link readouts of imaging biomarkers to their underlying molecular pathways with the aim of guiding clinical diagnosis, prognosis and even target identification in drug discovery for Alzheimer's disease. PMID:24287435

Inactivation of the Parietal Reach Region Causes Optic Ataxia, Impairing Reaches but Not Saccades

PubMed Central

Hwang, Eun Jung; Hauschild, Markus; Wilke, Melanie; Andersen, Richard A.

2013-01-01

SUMMARY Lesions in human posterior parietal cortex can cause optic ataxia (OA), in which reaches but not saccades to visual objects are impaired, suggesting separate visuomotor pathways for the two effectors. In monkeys, one potentially crucial area for reach control is the parietal reach region (PRR), in which neurons respond preferentially during reach planning as compared to saccade planning. However, direct causal evidence linking the monkey PRR to the deficits observed in OA is missing. We thus inactivated part of the macaque PRR, in the medial wall of the intraparietal sulcus, and produced the hallmarks of OA, misreaching for peripheral targets but unimpaired saccades. Furthermore, reach errors were larger for the targets preferred by the neural population local to the injection site. These results demonstrate that PRR is causally involved in reach-specific visuomotor pathways, and reach goal disruption in PRR can be a neural basis of OA. PMID:23217749

'What' Is Happening in the Dorsal Visual Pathway.

PubMed

Freud, Erez; Plaut, David C; Behrmann, Marlene

2016-10-01

The cortical visual system is almost universally thought to be segregated into two anatomically and functionally distinct pathways: a ventral occipitotemporal pathway that subserves object perception, and a dorsal occipitoparietal pathway that subserves object localization and visually guided action. Accumulating evidence from both human and non-human primate studies, however, challenges this binary distinction and suggests that regions in the dorsal pathway contain object representations that are independent of those in ventral cortex and that play a functional role in object perception. We review here the evidence implicating dorsal object representations, and we propose an account of the anatomical organization, functional contributions, and origins of these representations in the service of perception. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Quantative Adverse Outcome Pathway Linking Aromatase Inhibition in Fathead Minnows with Population Dynamics

EPA Science Inventory

A Quantitative Adverse Outcome Pathway Linking Aromatase Inhibition in Fathead Minnows with Population DynamicsAn adverse outcome pathway (AOP) is a qualitative description linking a molecular initiating event (MIE) with measureable key events leading to an adverse outcome (AO). ...

Visual Pathway Deficit in Female Fragile X Premutation Carriers: A Potential Endophenotype

ERIC Educational Resources Information Center

Keri, Szabolcs; Benedek, Gyorgy

2009-01-01

Previous studies indicated impaired magnocellular (M) and relatively spared parvocellular (P) visual pathway functioning in patients with fragile X syndrome. In this study, we assessed M and P pathways in 22 female fragile X premutation carriers with normal intelligence and in 20 healthy non-carrier controls. Testing procedure included visual…

The multiple sclerosis visual pathway cohort: understanding neurodegeneration in MS.

PubMed

Martínez-Lapiscina, Elena H; Fraga-Pumar, Elena; Gabilondo, Iñigo; Martínez-Heras, Eloy; Torres-Torres, Ruben; Ortiz-Pérez, Santiago; Llufriu, Sara; Tercero, Ana; Andorra, Magi; Roca, Marc Figueras; Lampert, Erika; Zubizarreta, Irati; Saiz, Albert; Sanchez-Dalmau, Bernardo; Villoslada, Pablo

2014-12-15

Multiple Sclerosis (MS) is an immune-mediated disease of the Central Nervous System with two major underlying etiopathogenic processes: inflammation and neurodegeneration. The latter determines the prognosis of this disease. MS is the main cause of non-traumatic disability in middle-aged populations. The MS-VisualPath Cohort was set up to study the neurodegenerative component of MS using advanced imaging techniques by focusing on analysis of the visual pathway in a middle-aged MS population in Barcelona, Spain. We started the recruitment of patients in the early phase of MS in 2010 and it remains permanently open. All patients undergo a complete neurological and ophthalmological examination including measurements of physical and disability (Expanded Disability Status Scale; Multiple Sclerosis Functional Composite and neuropsychological tests), disease activity (relapses) and visual function testing (visual acuity, color vision and visual field). The MS-VisualPath protocol also assesses the presence of anxiety and depressive symptoms (Hospital Anxiety and Depression Scale), general quality of life (SF-36) and visual quality of life (25-Item National Eye Institute Visual Function Questionnaire with the 10-Item Neuro-Ophthalmic Supplement). In addition, the imaging protocol includes both retinal (Optical Coherence Tomography and Wide-Field Fundus Imaging) and brain imaging (Magnetic Resonance Imaging). Finally, multifocal Visual Evoked Potentials are used to perform neurophysiological assessment of the visual pathway. The analysis of the visual pathway with advance imaging and electrophysilogical tools in parallel with clinical information will provide significant and new knowledge regarding neurodegeneration in MS and provide new clinical and imaging biomarkers to help monitor disease progression in these patients.

Web accessibility support for visually impaired users using link content analysis.

PubMed

Iwata, Hajime; Kobayashi, Naofumi; Tachibana, Kenji; Shirogane, Junko; Fukazawa, Yoshiaki

2013-12-01

Web pages are used for a variety of purposes. End users must understand dynamically changing content and sequentially follow page links to find desired material, requiring significant time and effort. However, for visually impaired users using screen readers, it can be difficult to find links to web pages when link text and alternative text descriptions are inappropriate. Our method supports the discovery of content by analyzing 8 categories of link types, and allows visually impaired users to be aware of the content represented by links in advance. This facilitates end users access to necessary information on web pages. Our method of classifying web page links is therefore effective as a means of evaluating accessibility.

Long-term effects of neonatal hypoxia-ischemia on structural and physiological integrity of the eye and visual pathway by multimodal MRI.

PubMed

Chan, Kevin C; Kancherla, Swarupa; Fan, Shu-Juan; Wu, Ed X

2014-12-09

Neonatal hypoxia-ischemia is a major cause of brain damage in infants and may frequently present visual impairments. Although advancements in perinatal care have increased survival, the pathogenesis of hypoxic-ischemic injury and the long-term consequences to the visual system remain unclear. We hypothesized that neonatal hypoxia-ischemia can lead to chronic, MRI-detectable structural and physiological alterations in both the eye and the brain's visual pathways. Eight Sprague-Dawley rats underwent ligation of the left common carotid artery followed by hypoxia for 2 hours at postnatal day 7. One year later, T2-weighted MRI, gadolinium-enhanced MRI, chromium-enhanced MRI, manganese-enhanced MRI, and diffusion tensor MRI (DTI) of the visual system were evaluated and compared between opposite hemispheres using a 7-Tesla scanner. Within the eyeball, systemic gadolinium administration revealed aqueous-vitreous or blood-ocular barrier leakage only in the ipsilesional left eye despite comparable aqueous humor dynamics in the anterior chamber of both eyes. Binocular intravitreal chromium injection showed compromised retinal integrity in the ipsilesional eye. Despite total loss of the ipsilesional visual cortex, both retinocollicular and retinogeniculate pathways projected from the contralesional eye toward ipsilesional visual cortex possessed stronger anterograde manganese transport and less disrupted structural integrity in DTI compared with the opposite hemispheres. High-field, multimodal MRI demonstrated in vivo the long-term structural and physiological deficits in the eye and brain's visual pathways after unilateral neonatal hypoxic-ischemic injury. The remaining retinocollicular and retinogeniculate pathways appeared to be more vulnerable to anterograde degeneration from eye injury than retrograde, transsynaptic degeneration from visual cortex injury. Copyright 2015 The Association for Research in Vision and Ophthalmology, Inc.

Long-Term Effects of Neonatal Hypoxia-Ischemia on Structural and Physiological Integrity of the Eye and Visual Pathway by Multimodal MRI

PubMed Central

Chan, Kevin C.; Kancherla, Swarupa; Fan, Shu-Juan; Wu, Ed X.

2015-01-01

Purpose. Neonatal hypoxia-ischemia is a major cause of brain damage in infants and may frequently present visual impairments. Although advancements in perinatal care have increased survival, the pathogenesis of hypoxic-ischemic injury and the long-term consequences to the visual system remain unclear. We hypothesized that neonatal hypoxia-ischemia can lead to chronic, MRI-detectable structural and physiological alterations in both the eye and the brain's visual pathways. Methods. Eight Sprague-Dawley rats underwent ligation of the left common carotid artery followed by hypoxia for 2 hours at postnatal day 7. One year later, T2-weighted MRI, gadolinium-enhanced MRI, chromium-enhanced MRI, manganese-enhanced MRI, and diffusion tensor MRI (DTI) of the visual system were evaluated and compared between opposite hemispheres using a 7-Tesla scanner. Results. Within the eyeball, systemic gadolinium administration revealed aqueous-vitreous or blood-ocular barrier leakage only in the ipsilesional left eye despite comparable aqueous humor dynamics in the anterior chamber of both eyes. Binocular intravitreal chromium injection showed compromised retinal integrity in the ipsilesional eye. Despite total loss of the ipsilesional visual cortex, both retinocollicular and retinogeniculate pathways projected from the contralesional eye toward ipsilesional visual cortex possessed stronger anterograde manganese transport and less disrupted structural integrity in DTI compared with the opposite hemispheres. Conclusions. High-field, multimodal MRI demonstrated in vivo the long-term structural and physiological deficits in the eye and brain's visual pathways after unilateral neonatal hypoxic-ischemic injury. The remaining retinocollicular and retinogeniculate pathways appeared to be more vulnerable to anterograde degeneration from eye injury than retrograde, transsynaptic degeneration from visual cortex injury. PMID:25491295

Reduction in Neural Performance following Recovery from Anoxic Stress Is Mimicked by AMPK Pathway Activation

PubMed Central

Money, Tomas G. A.; Sproule, Michael K. J.; Hamour, Amr F.; Robertson, R. Meldrum

2014-01-01

Nervous systems are energetically expensive to operate and maintain. Both synaptic and action potential signalling require a significant investment to maintain ion homeostasis. We have investigated the tuning of neural performance following a brief period of anoxia in a well-characterized visual pathway in the locust, the LGMD/DCMD looming motion-sensitive circuit. We hypothesised that the energetic cost of signalling can be dynamically modified by cellular mechanisms in response to metabolic stress. We examined whether recovery from anoxia resulted in a decrease in excitability of the electrophysiological properties in the DCMD neuron. We further examined the effect of these modifications on behavioural output. We show that recovery from anoxia affects metabolic rate, flight steering behaviour, and action potential properties. The effects of anoxia on action potentials can be mimicked by activation of the AMPK metabolic pathway. We suggest this is evidence of a coordinated cellular mechanism to reduce neural energetic demand following an anoxic stress. Together, this represents a dynamically-regulated means to link the energetic demands of neural signaling with the environmental constraints faced by the whole animal. PMID:24533112

Reduction in neural performance following recovery from anoxic stress is mimicked by AMPK pathway activation.

PubMed

Money, Tomas G A; Sproule, Michael K J; Hamour, Amr F; Robertson, R Meldrum

2014-01-01

Nervous systems are energetically expensive to operate and maintain. Both synaptic and action potential signalling require a significant investment to maintain ion homeostasis. We have investigated the tuning of neural performance following a brief period of anoxia in a well-characterized visual pathway in the locust, the LGMD/DCMD looming motion-sensitive circuit. We hypothesised that the energetic cost of signalling can be dynamically modified by cellular mechanisms in response to metabolic stress. We examined whether recovery from anoxia resulted in a decrease in excitability of the electrophysiological properties in the DCMD neuron. We further examined the effect of these modifications on behavioural output. We show that recovery from anoxia affects metabolic rate, flight steering behaviour, and action potential properties. The effects of anoxia on action potentials can be mimicked by activation of the AMPK metabolic pathway. We suggest this is evidence of a coordinated cellular mechanism to reduce neural energetic demand following an anoxic stress. Together, this represents a dynamically-regulated means to link the energetic demands of neural signaling with the environmental constraints faced by the whole animal.

CoPub: a literature-based keyword enrichment tool for microarray data analysis.

PubMed

Frijters, Raoul; Heupers, Bart; van Beek, Pieter; Bouwhuis, Maurice; van Schaik, René; de Vlieg, Jacob; Polman, Jan; Alkema, Wynand

2008-07-01

Medline is a rich information source, from which links between genes and keywords describing biological processes, pathways, drugs, pathologies and diseases can be extracted. We developed a publicly available tool called CoPub that uses the information in the Medline database for the biological interpretation of microarray data. CoPub allows batch input of multiple human, mouse or rat genes and produces lists of keywords from several biomedical thesauri that are significantly correlated with the set of input genes. These lists link to Medline abstracts in which the co-occurring input genes and correlated keywords are highlighted. Furthermore, CoPub can graphically visualize differentially expressed genes and over-represented keywords in a network, providing detailed insight in the relationships between genes and keywords, and revealing the most influential genes as highly connected hubs. CoPub is freely accessible at http://services.nbic.nl/cgi-bin/copub/CoPub.pl.

The dorsal "action" pathway.

PubMed

Gallivan, Jason P; Goodale, Melvyn A

2018-01-01

In 1992, Goodale and Milner proposed a division of labor in the visual pathways of the primate cerebral cortex. According to their account, the ventral pathway, which projects to occipitotemporal cortex, constructs our visual percepts, while the dorsal pathway, which projects to posterior parietal cortex, mediates the visual control of action. Although the framing of the two-visual-system hypothesis has not been without controversy, it is clear that vision for action and vision for perception have distinct computational requirements, and significant support for the proposed neuroanatomic division has continued to emerge over the last two decades from human neuropsychology, neuroimaging, behavioral psychophysics, and monkey neurophysiology. In this chapter, we review much of this evidence, with a particular focus on recent findings from human neuroimaging and monkey neurophysiology, demonstrating a specialized role for parietal cortex in visually guided behavior. But even though the available evidence suggests that dedicated circuits mediate action and perception, in order to produce adaptive goal-directed behavior there must be a close coupling and seamless integration of information processing across these two systems. We discuss such ventral-dorsal-stream interactions and argue that the two pathways play different, yet complementary, roles in the production of skilled behavior. Copyright © 2018 Elsevier B.V. All rights reserved.

Contrast Sensitivity for Motion Detection and Direction Discrimination in Adolescents with Autism Spectrum Disorders and Their Siblings

ERIC Educational Resources Information Center

Koh, Hwan Cui; Milne, Elizabeth; Dobkins, Karen

2010-01-01

The magnocellular (M) pathway hypothesis proposes that impaired visual motion perception observed in individuals with Autism Spectrum Disorders (ASD) might be mediated by atypical functioning of the subcortical M pathway, as this pathway provides the bulk of visual input to cortical motion detectors. To test this hypothesis, we measured luminance…

Clinical anatomy and imaging of the cranial nerves and skull base.

PubMed

Jha, Ruchira M; Klein, Joshua P

2012-09-01

Evaluation of patients with cranial neuropathies requires an understanding of brainstem anatomy and nerve pathways. Advances in neuroimaging, particularly high spatial resolution magnetic resonance imaging (MRI), have enabled visualization of these tiny structures and their related pathology. This review provides an approach toward using imaging in the evaluation of cranial nerve (CN) and skull base anatomy and pathology. Because brainstem nuclei are inextricably linked to the information contained within CNs, they are briefly mentioned whenever relevant; however, a comprehensive discussion of brainstem syndromes is beyond the scope of this review. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

VISIBIOweb: visualization and layout services for BioPAX pathway models

PubMed Central

Dilek, Alptug; Belviranli, Mehmet E.; Dogrusoz, Ugur

2010-01-01

With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, web-based pathway visualization and layout service for pathway models in BioPAX format. With VISIBIOweb, one can obtain well-laid-out views of pathway models using the standard notation of the Systems Biology Graphical Notation (SBGN), and can embed such views within one's web pages as desired. Pathway views may be navigated using zoom and scroll tools; pathway object properties, including any external database references available in the data, may be inspected interactively. The automatic layout component of VISIBIOweb may also be accessed programmatically from other tools using Hypertext Transfer Protocol (HTTP). The web site is free and open to all users and there is no login requirement. It is available at: http://visibioweb.patika.org. PMID:20460470

Beyond sensory images: Object-based representation in the human ventral pathway

PubMed Central

Pietrini, Pietro; Furey, Maura L.; Ricciardi, Emiliano; Gobbini, M. Ida; Wu, W.-H. Carolyn; Cohen, Leonardo; Guazzelli, Mario; Haxby, James V.

2004-01-01

We investigated whether the topographically organized, category-related patterns of neural response in the ventral visual pathway are a representation of sensory images or a more abstract representation of object form that is not dependent on sensory modality. We used functional MRI to measure patterns of response evoked during visual and tactile recognition of faces and manmade objects in sighted subjects and during tactile recognition in blind subjects. Results showed that visual and tactile recognition evoked category-related patterns of response in a ventral extrastriate visual area in the inferior temporal gyrus that were correlated across modality for manmade objects. Blind subjects also demonstrated category-related patterns of response in this “visual” area, and in more ventral cortical regions in the fusiform gyrus, indicating that these patterns are not due to visual imagery and, furthermore, that visual experience is not necessary for category-related representations to develop in these cortices. These results demonstrate that the representation of objects in the ventral visual pathway is not simply a representation of visual images but, rather, is a representation of more abstract features of object form. PMID:15064396

Visual circuits of the avian telencephalon: evolutionary implications

NASA Technical Reports Server (NTRS)

Shimizu, T.; Bowers, A. N.

1999-01-01

Birds and primates are vertebrates that possess the most advanced, efficient visual systems. Although lineages leading to these two classes were separated about 300 million years ago, there are striking similarities in their underlying neural mechanisms for visual processing. This paper discusses such similarities with special emphasis on the visual circuits in the avian telencephalon. These similarities include: (1) the existence of two parallel visual pathways and their distinct telencephalic targets, (2) anatomical and functional segregation within the visual pathways, (3) laminar organization of the telencephalic targets of the pathways (e.g. striate cortex in primates), and (4) possible interactions between multiple visual areas. Additional extensive analyses are necessary to determine whether these similarities are due to inheritance from a common ancestral stock or the consequences of convergent evolution based on adaptive response to similar selective pressures. Nevertheless, such a comparison is important to identify the general and specific principles of visual processing in amniotes (reptiles, birds, and mammals). Furthermore, these principles in turn will provide a critical foundation for understanding the evolution of the brain in amniotes.

Interleukins and their signaling pathways in the Reactome biological pathway database.

PubMed

Jupe, Steve; Ray, Keith; Roca, Corina Duenas; Varusai, Thawfeek; Shamovsky, Veronica; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-04-01

There is a wealth of biological pathway information available in the scientific literature, but it is spread across many thousands of publications. Alongside publications that contain definitive experimental discoveries are many others that have been dismissed as spurious, found to be irreproducible, or are contradicted by later results and consequently now considered controversial. Many descriptions and images of pathways are incomplete stylized representations that assume the reader is an expert and familiar with the established details of the process, which are consequently not fully explained. Pathway representations in publications frequently do not represent a complete, detailed, and unambiguous description of the molecules involved; their precise posttranslational state; or a full account of the molecular events they undergo while participating in a process. Although this might be sufficient to be interpreted by an expert reader, the lack of detail makes such pathways less useful and difficult to understand for anyone unfamiliar with the area and of limited use as the basis for computational models. Reactome was established as a freely accessible knowledge base of human biological pathways. It is manually populated with interconnected molecular events that fully detail the molecular participants linked to published experimental data and background material by using a formal and open data structure that facilitates computational reuse. These data are accessible on a Web site in the form of pathway diagrams that have descriptive summaries and annotations and as downloadable data sets in several formats that can be reused with other computational tools. The entire database and all supporting software can be downloaded and reused under a Creative Commons license. Pathways are authored by expert biologists who work with Reactome curators and editorial staff to represent the consensus in the field. Pathways are represented as interactive diagrams that include as much molecular detail as possible and are linked to literature citations that contain supporting experimental details. All newly created events undergo a peer-review process before they are added to the database and made available on the associated Web site. New content is added quarterly. The 63rd release of Reactome in December 2017 contains 10,996 human proteins participating in 11,426 events in 2,179 pathways. In addition, analytic tools allow data set submission for the identification and visualization of pathway enrichment and representation of expression profiles as an overlay on Reactome pathways. Protein-protein and compound-protein interactions from several sources, including custom user data sets, can be added to extend pathways. Pathway diagrams and analytic result displays can be downloaded as editable images, human-readable reports, and files in several standard formats that are suitable for computational reuse. Reactome content is available programmatically through a REpresentational State Transfer (REST)-based content service and as a Neo4J graph database. Signaling pathways for IL-1 to IL-38 are hierarchically classified within the pathway "signaling by interleukins." The classification used is largely derived from Akdis et al. The addition to Reactome of a complete set of the known human interleukins, their receptors, and established signaling pathways linked to annotations of relevant aspects of immune function provides a significant computationally accessible resource of information about this important family. This information can be extended easily as new discoveries become accepted as the consensus in the field. A key aim for the future is to increase coverage of gene expression changes induced by interleukin signaling. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

The evolution of concepts of color vision.

PubMed

Lee, Barry B

2008-07-01

The evolution of ideas about the way we see color was closely linked to physical theories of light. Proponents of both corpuscular and wave theories viewed light as a continuous spectrum. This was not easily reconciled with the fact that, for the human eye, all colors can be matched by mixture of three primaries. Physicists such as Mayer who described trichromatic color matching often assumed that there were just three types of rays in the spectrum. This argument was finally resolved by Thomas Young, who noted that trichromatic color matching was consistent with a continuous spectrum if there were just three receptors in the eye. This kind of conceptual mistake, in this case the confusion of the properties of the visual system with physical properties of light, has been common in the history of color science. As another example, the idea of trichromacy was disputed by those who viewed color sensations as opponent processes, red-green, blue-yellow and black-white. The discovery of color-opponent neurons in the visual pathway has partly resolved this dilemma. Much of the physiological substrate of the way we detect and distinguish colors is now established, but the link between the signals leaving the retina and the way we name and order colors is still poorly defined.

The evolution of concepts of color vision

PubMed Central

Lee, Barry. B.

2010-01-01

The evolution of ideas about the way we see color was closely linked to physical theories of light. Proponents of both corpuscular and wave theories viewed light as a continuous spectrum. This was not easily reconciled with the fact that, for the human eye, all colors can be matched by mixture of three primaries. Physicists such as Mayer who described trichromatic color matching often assumed that there were just three types of rays in the spectrum. This argument was finally resolved by Thomas Young, who noted that trichromatic color matching was consistent with a continuous spectrum if there were just three receptors in the eye. This kind of conceptual mistake, in this case the confusion of the properties of the visual system with physical properties of light, has been common in the history of color science. As another example, the idea of trichromacy was disputed by those who viewed color sensations as opponent processes, red-green, blue-yellow and black-white. The discovery of color-opponent neurons in the visual pathway has partly resolved this dilemma. Much of the physiological substrate of the way we detect and distinguish colors is now established, but the link between the signals leaving the retina and the way we name and order colors is still poorly defined. PMID:21593994

Visual-Cerebellar Pathways and Their Roles in the Control of Avian Flight.

PubMed

Wylie, Douglas R; Gutiérrez-Ibáñez, Cristián; Gaede, Andrea H; Altshuler, Douglas L; Iwaniuk, Andrew N

2018-01-01

In this paper, we review the connections and physiology of visual pathways to the cerebellum in birds and consider their role in flight. We emphasize that there are two visual pathways to the cerebellum. One is to the vestibulocerebellum (folia IXcd and X) that originates from two retinal-recipient nuclei that process optic flow: the nucleus of the basal optic root (nBOR) and the pretectal nucleus lentiformis mesencephali (LM). The second is to the oculomotor cerebellum (folia VI-VIII), which receives optic flow information, mainly from LM, but also local visual motion information from the optic tectum, and other visual information from the ventral lateral geniculate nucleus (Glv). The tectum, LM and Glv are all intimately connected with the pontine nuclei, which also project to the oculomotor cerebellum. We believe this rich integration of visual information in the cerebellum is important for analyzing motion parallax that occurs during flight. Finally, we extend upon a suggestion by Ibbotson (2017) that the hypertrophy that is observed in LM in hummingbirds might be due to an increase in the processing demands associated with the pathway to the oculomotor cerebellum as they fly through a cluttered environment while feeding.

The effects of link format and screen location on visual search of web pages.

PubMed

Ling, Jonathan; Van Schaik, Paul

2004-06-22

Navigation of web pages is of critical importance to the usability of web-based systems such as the World Wide Web and intranets. The primary means of navigation is through the use of hyperlinks. However, few studies have examined the impact of the presentation format of these links on visual search. The present study used a two-factor mixed measures design to investigate whether there was an effect of link format (plain text, underlined, bold, or bold and underlined) upon speed and accuracy of visual search and subjective measures in both the navigation and content areas of web pages. An effect of link format on speed of visual search for both hits and correct rejections was found. This effect was observed in the navigation and the content areas. Link format did not influence accuracy in either screen location. Participants showed highest preference for links that were in bold and underlined, regardless of screen area. These results are discussed in the context of visual search processes and design recommendations are given.

Emissions Scenario Portal for Visualization of Low Carbon Pathways

NASA Astrophysics Data System (ADS)

Friedrich, J.; Hennig, R. J.; Mountford, H.; Altamirano, J. C.; Ge, M.; Fransen, T.

2016-12-01

This proposal for a presentation is centered around a new project which is developed collaboratively by the World Resources Institute (WRI), Google Inc., and Deep Decarbonization Pathways Project (DDPP). The project aims to develop an online, open portal, the Emissions Scenario Portal (ESP),to enable users to easily visualize a range of future greenhouse gas emission pathways linked to different scenarios of economic and energy developments, drawing from a variety of modeling tools. It is targeted to users who are not modelling experts, but instead policy analysts or advisors, investment analysts, and similar who draw on modelled scenarios to inform their work, and who can benefit from better access to, and transparency around, the wide range of emerging scenarios on ambitious climate action. The ESP will provide information from scenarios in a visually appealing and easy-to-understand manner that enable these users to recognize the opportunities to reduce GHG emissions, the implications of the different scenarios, and the underlying assumptions. To facilitate the application of the portal and tools in policy dialogues, a series of country-specific and potentially sector-specific workshops with key decision-makers and analysts, supported by relevant analysis, will be organized by the key partners and also in broader collaboration with others who might wish to convene relevant groups around the information. This project will provide opportunities for modelers to increase their outreach and visibility in the public space and to directly interact with key audiences of emissions scenarios, such as policy analysts and advisors. The information displayed on the portal will cover a wide range of indicators, sectors and important scenario characteristics such as macroeconomic information, emission factors and policy as well as technology assumptions in order to facilitate comparison. These indicators have been selected based on existing standards (such as the IIASA AR5 database, the Greenhouse Gas Protocol and accounting literature) and stakeholder consultations. Examples for use cases include: technical advisers for governments NGO/Civil Society advocates Investors and bankers Modelers and academics Business sustainability officers

Real-time interactive tractography analysis for multimodal brain visualization tool: MultiXplore

NASA Astrophysics Data System (ADS)

Bakhshmand, Saeed M.; de Ribaupierre, Sandrine; Eagleson, Roy

2017-03-01

Most debilitating neurological disorders can have anatomical origins. Yet unlike other body organs, the anatomy alone cannot easily provide an understanding of brain functionality. In fact, addressing the challenge of linking structural and functional connectivity remains in the frontiers of neuroscience. Aggregating multimodal neuroimaging datasets may be critical for developing theories that span brain functionality, global neuroanatomy and internal microstructures. Functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) are main such techniques that are employed to investigate the brain under normal and pathological conditions. FMRI records blood oxygenation level of the grey matter (GM), whereas DTI is able to reveal the underlying structure of the white matter (WM). Brain global activity is assumed to be an integration of GM functional hubs and WM neural pathways that serve to connect them. In this study we developed and evaluated a two-phase algorithm. This algorithm is employed in a 3D interactive connectivity visualization framework and helps to accelerate clustering of virtual neural pathways. In this paper, we will detail an algorithm that makes use of an index-based membership array formed for a whole brain tractography file and corresponding parcellated brain atlas. Next, we demonstrate efficiency of the algorithm by measuring required times for extracting a variety of fiber clusters, which are chosen in such a way to resemble all sizes probable output data files that algorithm will generate. The proposed algorithm facilitates real-time visual inspection of neuroimaging data to further the discovery in structure-function relationship of the brain networks.

Alternate Metabolic Programs Define Regional Variation of Relevant Biological Features in Renal Cell Carcinoma Progression.

PubMed

Brooks, Samira A; Khandani, Amir H; Fielding, Julia R; Lin, Weili; Sills, Tiffany; Lee, Yueh; Arreola, Alexandra; Milowsky, Mathew I; Wallen, Eric M; Woods, Michael E; Smith, Angie B; Nielsen, Mathew E; Parker, Joel S; Lalush, David S; Rathmell, W Kimryn

2016-06-15

Clear cell renal cell carcinoma (ccRCC) has recently been redefined as a highly heterogeneous disease. In addition to genetic heterogeneity, the tumor displays risk variability for developing metastatic disease, therefore underscoring the urgent need for tissue-based prognostic strategies applicable to the clinical setting. We have recently employed the novel PET/magnetic resonance (MR) image modality to enrich our understanding of how tumor heterogeneity can relate to gene expression and tumor biology to assist in defining individualized treatment plans. ccRCC patients underwent PET/MR imaging, and these images subsequently used to identify areas of varied intensity for sampling. Samples from 8 patients were subjected to histologic, immunohistochemical, and microarray analysis. Tumor subsamples displayed a range of heterogeneity for common features of hypoxia-inducible factor expression and microvessel density, as well as for features closely linked to metabolic processes, such as GLUT1 and FBP1. In addition, gene signatures linked with disease risk (ccA and ccB) also demonstrated variable heterogeneity, with most tumors displaying a dominant panel of features across the sampled regions. Intriguingly, the ccA- and ccB-classified samples corresponded with metabolic features and functional imaging levels. These correlations further linked a variety of metabolic pathways (i.e., the pentose phosphate and mTOR pathways) with the more aggressive, and glucose avid ccB subtype. Higher tumor dependency on exogenous glucose accompanies the development of features associated with the poor risk ccB subgroup. Linking these panels of features may provide the opportunity to create functional maps to enable enhanced visualization of the heterogeneous biologic processes of an individual's disease. Clin Cancer Res; 22(12); 2950-9. ©2016 AACR. ©2016 American Association for Cancer Research.

Smelling directions: Olfaction modulates ambiguous visual motion perception

PubMed Central

Kuang, Shenbing; Zhang, Tao

2014-01-01

Senses of smells are often accompanied by simultaneous visual sensations. Previous studies have documented enhanced olfactory performance with concurrent presence of congruent color- or shape- related visual cues, and facilitated visual object perception when congruent smells are simultaneously present. These visual object-olfaction interactions suggest the existences of couplings between the olfactory pathway and the visual ventral processing stream. However, it is not known if olfaction can modulate visual motion perception, a function that is related to the visual dorsal stream. We tested this possibility by examining the influence of olfactory cues on the perceptions of ambiguous visual motion signals. We showed that, after introducing an association between motion directions and olfactory cues, olfaction could indeed bias ambiguous visual motion perceptions. Our result that olfaction modulates visual motion processing adds to the current knowledge of cross-modal interactions and implies a possible functional linkage between the olfactory system and the visual dorsal pathway. PMID:25052162

Multisensory training can promote or impede visual perceptual learning of speech stimuli: visual-tactile vs. visual-auditory training.

PubMed

Eberhardt, Silvio P; Auer, Edward T; Bernstein, Lynne E

2014-01-01

In a series of studies we have been investigating how multisensory training affects unisensory perceptual learning with speech stimuli. Previously, we reported that audiovisual (AV) training with speech stimuli can promote auditory-only (AO) perceptual learning in normal-hearing adults but can impede learning in congenitally deaf adults with late-acquired cochlear implants. Here, impeder and promoter effects were sought in normal-hearing adults who participated in lipreading training. In Experiment 1, visual-only (VO) training on paired associations between CVCVC nonsense word videos and nonsense pictures demonstrated that VO words could be learned to a high level of accuracy even by poor lipreaders. In Experiment 2, visual-auditory (VA) training in the same paradigm but with the addition of synchronous vocoded acoustic speech impeded VO learning of the stimuli in the paired-associates paradigm. In Experiment 3, the vocoded AO stimuli were shown to be less informative than the VO speech. Experiment 4 combined vibrotactile speech stimuli with the visual stimuli during training. Vibrotactile stimuli were shown to promote visual perceptual learning. In Experiment 5, no-training controls were used to show that training with visual speech carried over to consonant identification of untrained CVCVC stimuli but not to lipreading words in sentences. Across this and previous studies, multisensory training effects depended on the functional relationship between pathways engaged during training. Two principles are proposed to account for stimulus effects: (1) Stimuli presented to the trainee's primary perceptual pathway will impede learning by a lower-rank pathway. (2) Stimuli presented to the trainee's lower rank perceptual pathway will promote learning by a higher-rank pathway. The mechanisms supporting these principles are discussed in light of multisensory reverse hierarchy theory (RHT).

Tactile spatial working memory activates the dorsal extrastriate cortical pathway in congenitally blind individuals.

PubMed

Bonino, D; Ricciardi, E; Sani, L; Gentili, C; Vanello, N; Guazzelli, M; Vecchi, T; Pietrini, P

2008-09-01

In sighted individuals, both the visual and tactile version of the same spatial working memory task elicited neural responses in the dorsal "where" cortical pathway (Ricciardi et al., 2006). Whether the neural response during the tactile working memory task is due to visually-based spatial imagery or rather reflects a more abstract, supramodal organization of the dorsal cortical pathway remains to be determined. To understand the role of visual experience on the functional organization of the dorsal cortical stream, using functional magnetic resonance imaging (fMRI) here we examined brain response in four individuals with congenital or early blindness and no visual recollection, while they performed the same tactile spatial working memory task, a one-back recognition of 2D and 3D matrices. The blind subjects showed a significant activation in bilateral posterior parietal cortex, dorsolateral and inferior prefrontal areas, precuneus, lateral occipital cortex, and cerebellum. Thus, dorsal occipito-parietal areas are involved in mental imagery dealing with spatial components in subjects without prior visual experience and in response to a non-visual task. These data indicate that recruitment of the dorsal cortical pathway in response to the tactile spatial working memory task is not mediated by visually-based imagery and that visual experience is not a prerequisite for the development of a more abstract functional organization of the dorsal stream. These findings, along with previous data indicating a similar supramodal functional organization within the ventral cortical pathway and the motion processing brain regions, may contribute to explain how individuals who are born deprived of sight are able to interact effectively with the surrounding world.

Multisensory training can promote or impede visual perceptual learning of speech stimuli: visual-tactile vs. visual-auditory training

PubMed Central

Eberhardt, Silvio P.; Auer Jr., Edward T.; Bernstein, Lynne E.

2014-01-01

In a series of studies we have been investigating how multisensory training affects unisensory perceptual learning with speech stimuli. Previously, we reported that audiovisual (AV) training with speech stimuli can promote auditory-only (AO) perceptual learning in normal-hearing adults but can impede learning in congenitally deaf adults with late-acquired cochlear implants. Here, impeder and promoter effects were sought in normal-hearing adults who participated in lipreading training. In Experiment 1, visual-only (VO) training on paired associations between CVCVC nonsense word videos and nonsense pictures demonstrated that VO words could be learned to a high level of accuracy even by poor lipreaders. In Experiment 2, visual-auditory (VA) training in the same paradigm but with the addition of synchronous vocoded acoustic speech impeded VO learning of the stimuli in the paired-associates paradigm. In Experiment 3, the vocoded AO stimuli were shown to be less informative than the VO speech. Experiment 4 combined vibrotactile speech stimuli with the visual stimuli during training. Vibrotactile stimuli were shown to promote visual perceptual learning. In Experiment 5, no-training controls were used to show that training with visual speech carried over to consonant identification of untrained CVCVC stimuli but not to lipreading words in sentences. Across this and previous studies, multisensory training effects depended on the functional relationship between pathways engaged during training. Two principles are proposed to account for stimulus effects: (1) Stimuli presented to the trainee’s primary perceptual pathway will impede learning by a lower-rank pathway. (2) Stimuli presented to the trainee’s lower rank perceptual pathway will promote learning by a higher-rank pathway. The mechanisms supporting these principles are discussed in light of multisensory reverse hierarchy theory (RHT). PMID:25400566

Auditory and Visual Interhemispheric Communication in Musicians and Non-Musicians

PubMed Central

Woelfle, Rebecca; Grahn, Jessica A.

2013-01-01

The corpus callosum (CC) is a brain structure composed of axon fibres linking the right and left hemispheres. Musical training is associated with larger midsagittal cross-sectional area of the CC, suggesting that interhemispheric communication may be faster in musicians. Here we compared interhemispheric transmission times (ITTs) for musicians and non-musicians. ITT was measured by comparing simple reaction times to stimuli presented to the same hemisphere that controlled a button-press response (uncrossed reaction time), or to the contralateral hemisphere (crossed reaction time). Both visual and auditory stimuli were tested. We predicted that the crossed-uncrossed difference (CUD) for musicians would be smaller than for non-musicians as a result of faster interhemispheric transfer times. We did not expect a difference in CUDs between the visual and auditory modalities for either musicians or non-musicians, as previous work indicates that interhemispheric transfer may happen through the genu of the CC, which contains motor fibres rather than sensory fibres. There were no significant differences in CUDs between musicians and non-musicians. However, auditory CUDs were significantly smaller than visual CUDs. Although this auditory-visual difference was larger in musicians than non-musicians, the interaction between modality and musical training was not significant. Therefore, although musical training does not significantly affect ITT, the crossing of auditory information between hemispheres appears to be faster than visual information, perhaps because subcortical pathways play a greater role for auditory interhemispheric transfer. PMID:24386382

Slow and fast visual motion channels have independent binocular-rivalry stages.

PubMed Central

van de Grind, W. A.; van Hof, P.; van der Smagt, M. J.; Verstraten, F. A.

2001-01-01

We have previously reported a transparent motion after-effect indicating that the human visual system comprises separate slow and fast motion channels. Here, we report that the presentation of a fast motion in one eye and a slow motion in the other eye does not result in binocular rivalry but in a clear percept of transparent motion. We call this new visual phenomenon 'dichoptic motion transparency' (DMT). So far only the DMT phenomenon and the two motion after-effects (the 'classical' motion after-effect, seen after motion adaptation on a static test pattern, and the dynamic motion after-effect, seen on a dynamic-noise test pattern) appear to isolate the channels completely. The speed ranges of the slow and fast channels overlap strongly and are observer dependent. A model is presented that links after-effect durations of an observer to the probability of rivalry or DMT as a function of dichoptic velocity combinations. Model results support the assumption of two highly independent channels showing only within-channel rivalry, and no rivalry or after-effect interactions between the channels. The finding of two independent motion vision channels, each with a separate rivalry stage and a private line to conscious perception, might be helpful in visualizing or analysing pathways to consciousness. PMID:11270442

Grohar: Automated Visualization of Genome-Scale Metabolic Models and Their Pathways.

PubMed

Moškon, Miha; Zimic, Nikolaj; Mraz, Miha

2018-05-01

Genome-scale metabolic models (GEMs) have become a powerful tool for the investigation of the entire metabolism of the organism in silico. These models are, however, often extremely hard to reconstruct and also difficult to apply to the selected problem. Visualization of the GEM allows us to easier comprehend the model, to perform its graphical analysis, to find and correct the faulty relations, to identify the parts of the system with a designated function, etc. Even though several approaches for the automatic visualization of GEMs have been proposed, metabolic maps are still manually drawn or at least require large amount of manual curation. We present Grohar, a computational tool for automatic identification and visualization of GEM (sub)networks and their metabolic fluxes. These (sub)networks can be specified directly by listing the metabolites of interest or indirectly by providing reference metabolic pathways from different sources, such as KEGG, SBML, or Matlab file. These pathways are identified within the GEM using three different pathway alignment algorithms. Grohar also supports the visualization of the model adjustments (e.g., activation or inhibition of metabolic reactions) after perturbations are induced.

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data.

PubMed

Hernández-de-Diego, Rafael; Tarazona, Sonia; Martínez-Mira, Carlos; Balzano-Nogueira, Leandro; Furió-Tarí, Pedro; Pappas, Georgios J; Conesa, Ana

2018-05-25

The increasing availability of multi-omic platforms poses new challenges to data analysis. Joint visualization of multi-omics data is instrumental in better understanding interconnections across molecular layers and in fully utilizing the multi-omic resources available to make biological discoveries. We present here PaintOmics 3, a web-based resource for the integrated visualization of multiple omic data types onto KEGG pathway diagrams. PaintOmics 3 combines server-end capabilities for data analysis with the potential of modern web resources for data visualization, providing researchers with a powerful framework for interactive exploration of their multi-omics information. Unlike other visualization tools, PaintOmics 3 covers a comprehensive pathway analysis workflow, including automatic feature name/identifier conversion, multi-layered feature matching, pathway enrichment, network analysis, interactive heatmaps, trend charts, and more. It accepts a wide variety of omic types, including transcriptomics, proteomics and metabolomics, as well as region-based approaches such as ATAC-seq or ChIP-seq data. The tool is freely available at www.paintomics.org.

A new neural framework for visuospatial processing.

PubMed

Kravitz, Dwight J; Saleem, Kadharbatcha S; Baker, Chris I; Mishkin, Mortimer

2011-04-01

The division of cortical visual processing into distinct dorsal and ventral streams is a key framework that has guided visual neuroscience. The characterization of the ventral stream as a 'What' pathway is relatively uncontroversial, but the nature of dorsal stream processing is less clear. Originally proposed as mediating spatial perception ('Where'), more recent accounts suggest it primarily serves non-conscious visually guided action ('How'). Here, we identify three pathways emerging from the dorsal stream that consist of projections to the prefrontal and premotor cortices, and a major projection to the medial temporal lobe that courses both directly and indirectly through the posterior cingulate and retrosplenial cortices. These three pathways support both conscious and non-conscious visuospatial processing, including spatial working memory, visually guided action and navigation, respectively.

PyPathway: Python Package for Biological Network Analysis and Visualization.

PubMed

Xu, Yang; Luo, Xiao-Chun

2018-05-01

Life science studies represent one of the biggest generators of large data sets, mainly because of rapid sequencing technological advances. Biological networks including interactive networks and human curated pathways are essential to understand these high-throughput data sets. Biological network analysis offers a method to explore systematically not only the molecular complexity of a particular disease but also the molecular relationships among apparently distinct phenotypes. Currently, several packages for Python community have been developed, such as BioPython and Goatools. However, tools to perform comprehensive network analysis and visualization are still needed. Here, we have developed PyPathway, an extensible free and open source Python package for functional enrichment analysis, network modeling, and network visualization. The network process module supports various interaction network and pathway databases such as Reactome, WikiPathway, STRING, and BioGRID. The network analysis module implements overrepresentation analysis, gene set enrichment analysis, network-based enrichment, and de novo network modeling. Finally, the visualization and data publishing modules enable users to share their analysis by using an easy web application. For package availability, see the first Reference.

Sand sources and transport pathways for the San Francisco Bay coastal system, based on X-ray diffraction mineralogy

USGS Publications Warehouse

Hein, James R.; Mizell, Kira; Barnard, Patrick L.; Barnard, P.L.; Jaffee, B.E.; Schoellhamer, D.H.

2013-01-01

The mineralogical compositions of 119 samples collected from throughout the San Francisco Bay coastal system, including bayfloor and seafloor, area beaches, cliff outcrops, and major drainages, were determined using X-ray diffraction (XRD). Comparison of the mineral concentrations and application of statistical cluster analysis of XRD spectra allowed for the determination of provenances and transport pathways. The use of XRD mineral identifications provides semi-quantitative compositions needed for comparisons of beach and offshore sands with potential cliff and river sources, but the innovative cluster analysis of XRD diffraction spectra provides a unique visualization of how groups of samples within the San Francisco Bay coastal system are related so that sand-sized sediment transport pathways can be inferred. The main vector for sediment transport as defined by the XRD analysis is from San Francisco Bay to the outer coast, where the sand then accumulates on the ebb tidal delta and also moves alongshore. This mineralogical link defines a critical pathway because large volumes of sediment have been removed from the Bay over the last century via channel dredging, aggregate mining, and borrow pit mining, with comparable volumes of erosion from the ebb tidal delta over the same period, in addition to high rates of shoreline retreat along the adjacent, open-coast beaches. Therefore, while previously only a temporal relationship was established, the transport pathway defined by mineralogical and geochemical tracers support the link between anthropogenic activities in the Bay and widespread erosion outside the Bay. The XRD results also establish the regional and local importance of sediment derived from cliff erosion, as well as both proximal and distal fluvial sources. This research is an important contribution to a broader provenance study aimed at identifying the driving forces for widespread geomorphic change in a heavily urbanized coastal-estuarine system.

It's all connected: Pathways in visual object recognition and early noun learning.

PubMed

Smith, Linda B

2013-11-01

A developmental pathway may be defined as the route, or chain of events, through which a new structure or function forms. For many human behaviors, including object name learning and visual object recognition, these pathways are often complex and multicausal and include unexpected dependencies. This article presents three principles of development that suggest the value of a developmental psychology that explicitly seeks to trace these pathways and uses empirical evidence on developmental dependencies among motor development, action on objects, visual object recognition, and object name learning in 12- to 24-month-old infants to make the case. The article concludes with a consideration of the theoretical implications of this approach. (PsycINFO Database Record (c) 2013 APA, all rights reserved).

Electropysiologic evaluation of the visual pathway in patients with multiple sclerosis.

PubMed

Rodriguez-Mena, Diego; Almarcegui, Carmen; Dolz, Isabel; Herrero, Raquel; Bambo, Maria P; Fernandez, Javier; Pablo, Luis E; Garcia-Martin, Elena

2013-08-01

To evaluate the ability of visual evoked potentials and pattern electroretinograms (PERG) to detect subclinical axonal damage in patients during the early diagnostic stage of multiple sclerosis (MS). The authors also compared the ability of optical coherence tomography (OCT), PERG, and visual evoked potentials to detect axonal loss in MS patients and correlated the functional and structural properties of the retinal nerve fiber layer. Two hundred twenty-eight eyes of 114 subjects (57 MS patients and 57 age- and sex-matched healthy controls) were included. The visual pathway was evaluated based on functional and structural assessments. All patients underwent a complete ophthalmic examination that included assessment of visual acuity, ocular motility, intraocular pressure, visual field, papillary morphology, OCT, visual evoked potentials, and PERG. Visual evoked potentials (P100 latency and amplitude), PERG (N95 amplitude and N95/P50 ratio), and OCT parameters differed significantly between MS patients and healthy subjects. Moderate significant correlations were found between visual evoked potentials or PERG parameters and OCT measurements. Axonal damage in ganglion cells of the visual pathway can be detected based on structural measures provided by OCT in MS patients and by the N95 component and N95/P50 index of PERG, thus providing good correlation between function and structure.

Leading High School Transformation for College and Career Success: A Guide for Developing a System of Linked Learning Pathways

ERIC Educational Resources Information Center

Stearns, Roman

2014-01-01

This ConnectEd Guide for Developing a System of Linked Learning Pathways will introduce school district leaders and their community partners to Linked Learning and a system of quality pathways that can transform high schools, instructional practice, and the student experience. Not intended to be prescriptive, this document can and should be…

Predicting Cortical Dark/Bright Asymmetries from Natural Image Statistics and Early Visual Transforms

PubMed Central

Cooper, Emily A.; Norcia, Anthony M.

2015-01-01

The nervous system has evolved in an environment with structure and predictability. One of the ubiquitous principles of sensory systems is the creation of circuits that capitalize on this predictability. Previous work has identified predictable non-uniformities in the distributions of basic visual features in natural images that are relevant to the encoding tasks of the visual system. Here, we report that the well-established statistical distributions of visual features -- such as visual contrast, spatial scale, and depth -- differ between bright and dark image components. Following this analysis, we go on to trace how these differences in natural images translate into different patterns of cortical input that arise from the separate bright (ON) and dark (OFF) pathways originating in the retina. We use models of these early visual pathways to transform natural images into statistical patterns of cortical input. The models include the receptive fields and non-linear response properties of the magnocellular (M) and parvocellular (P) pathways, with their ON and OFF pathway divisions. The results indicate that there are regularities in visual cortical input beyond those that have previously been appreciated from the direct analysis of natural images. In particular, several dark/bright asymmetries provide a potential account for recently discovered asymmetries in how the brain processes visual features, such as violations of classic energy-type models. On the basis of our analysis, we expect that the dark/bright dichotomy in natural images plays a key role in the generation of both cortical and perceptual asymmetries. PMID:26020624

Pathview Web: user friendly pathway visualization and data integration

PubMed Central

Pant, Gaurav; Bhavnasi, Yeshvant K.; Blanchard, Steven G.; Brouwer, Cory

2017-01-01

Abstract Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. PMID:28482075

The Role of Lamination in Neocortical Function

DTIC Science & Technology

1991-12-20

U. Studies of the Tectofugal System: Tectal pathways to the telencephalon in birds and mammals. The tecto-thalamo-telencephalic visual pathway is...significance of lamination of the telencephalon . Visual Structures and Integrated Functions, Research Notes in Neural Computing (Michael Arbib and J6rg

Multiple repair pathways mediate tolerance to chemotherapeutic cross-linking agents in vertebrate cells.

PubMed

Nojima, Kuniharu; Hochegger, Helfrid; Saberi, Alihossein; Fukushima, Toru; Kikuchi, Koji; Yoshimura, Michio; Orelli, Brian J; Bishop, Douglas K; Hirano, Seiki; Ohzeki, Mioko; Ishiai, Masamichi; Yamamoto, Kazuhiko; Takata, Minoru; Arakawa, Hiroshi; Buerstedde, Jean-Marie; Yamazoe, Mitsuyoshi; Kawamoto, Takuo; Araki, Kasumi; Takahashi, Jun A; Hashimoto, Nobuo; Takeda, Shunichi; Sonoda, Eiichiro

2005-12-15

Cross-linking agents that induce DNA interstrand cross-links (ICL) are widely used in anticancer chemotherapy. Yeast genetic studies show that nucleotide excision repair (NER), Rad6/Rad18-dependent postreplication repair, homologous recombination, and cell cycle checkpoint pathway are involved in ICL repair. To study the contribution of DNA damage response pathways in tolerance to cross-linking agents in vertebrates, we made a panel of gene-disrupted clones from chicken DT40 cells, each defective in a particular DNA repair or checkpoint pathway, and measured the sensitivities to cross-linking agents, including cis-diamminedichloroplatinum (II) (cisplatin), mitomycin C, and melphalan. We found that cells harboring defects in translesion DNA synthesis (TLS), Fanconi anemia complementation groups (FANC), or homologous recombination displayed marked hypersensitivity to all the cross-linking agents, whereas NER seemed to play only a minor role. This effect of replication-dependent repair pathways is distinctively different from the situation in yeast, where NER seems to play a major role in dealing with ICL. Cells deficient in Rev3, the catalytic subunit of TLS polymerase Polzeta, showed the highest sensitivity to cisplatin followed by fanc-c. Furthermore, epistasis analysis revealed that these two mutants work in the same pathway. Our genetic comprehensive study reveals a critical role for DNA repair pathways that release DNA replication block at ICLs in cellular tolerance to cross-linking agents and could be directly exploited in designing an effective chemotherapy.

Anatomical evidence for the influence of degenerating pathways on regenerating optic fibers following surgical manipulations in the visual system of the goldfish.

PubMed

Lo, R Y; Levine, R L

1981-04-06

We have used [3H]proline radioautography to trace regenerating optic fibers in the goldfish following: (1) the removal of the right tectal lobe and the right eye, and (2) the removal of both tectal lobes. Our results indicate that following the removal of the right tectal lobe and the right eye, both the denervated tectal efferent pathways, and the denervated visual pathways and terminal zones of the enucleated eye were penetrated by the regenerating optic fibers. In addition, following bilateral lobectomy, the denervated tectal efferent pathways were bilaterally penetrated by the regenerating fibers. Since, in both types of operations, these denervated pathways and terminal zones should undergo degeneration, our results support the suggestion that the presence of degenerating axonal debris and proliferating glia may play an important role in guiding regenerating optic fibers in the visual system of the goldfish.

Elaborate mapping of the posterior visual pathway in awake craniotomy.

PubMed

Shahar, Tal; Korn, Akiva; Barkay, Gal; Biron, Tali; Hadanny, Amir; Gazit, Tomer; Nossek, Erez; Ekstein, Margaret; Kesler, Anat; Ram, Zvi

2018-05-01

OBJECTIVE Resection of intraaxial tumors adjacent to the optic radiation (OR) may be associated with postoperative visual field (VF) deficits. Intraoperative navigation using MRI-based tractography and electrophysiological monitoring of the visual pathways may allow maximal resection while preserving visual function. In this study, the authors evaluated the value of visual pathway mapping in a series of patients undergoing awake craniotomy for tumor resection. METHODS A retrospective analysis of prospectively collected data was conducted in 18 patients who underwent an awake craniotomy for resection of intraaxial tumors involving or adjacent to the OR. Preoperative MRI-based tractography was used for intraoperative navigation, and intraoperative acquisition of 3D ultrasonography images was performed for real-time imaging and correction of brain shift. Goggles with light-emitting diodes were used as a standard visual stimulus. Direct cortical visual evoked potential (VEP) recording, subcortical recordings from the OR, and subcortical stimulation of the OR were used intraoperatively to assess visual function and proximity of the lesion to the OR. VFs were assessed pre- and postoperatively. RESULTS Baseline cortical VEP recordings were available for 14 patients (77.7%). No association was found between preoperative VF status and baseline presence of cortical VEPs (p = 0.27). Five of the 14 patients (35.7%) who underwent subcortical stimulation of the OR reported seeing phosphenes in the corresponding contralateral VF. There was a positive correlation (r = 0.899, p = 0.04) between the subcortical threshold stimulation intensity (3-11.5 mA) and the distance from the OR. Subcortical recordings from the OR demonstrated a typical VEP waveform in 10 of the 13 evaluated patients (76.9%). These waveforms were present only when recordings were obtained within 10 mm of the OR (p = 0.04). Seven patients (38.9%) had postoperative VF deterioration, and it was associated with a length of < 8 mm between the tumor and the OR (p = 0.05). CONCLUSIONS Intraoperative electrophysiological monitoring of the visual pathways is feasible but may be of limited value in preserving the functional integrity of the posterior visual pathways. Subcortical stimulation of the OR may identify the location of the OR when done in proximity to the pathways, but such proximity may be associated with increased risk of postoperative worsening of the VF deficit.

Linked exploratory visualizations for uncertain MR spectroscopy data

NASA Astrophysics Data System (ADS)

Feng, David; Kwock, Lester; Lee, Yueh; Taylor, Russell M., II

2010-01-01

We present a system for visualizing magnetic resonance spectroscopy (MRS) data sets. Using MRS, radiologists generate multiple 3D scalar fields of metabolite concentrations within the brain and compare them to anatomical magnetic resonance imaging. By understanding the relationship between metabolic makeup and anatomical structure, radiologists hope to better diagnose and treat tumors and lesions. Our system consists of three linked visualizations: a spatial glyph-based technique we call Scaled Data-Driven Spheres, a parallel coordinates visualization augmented to incorporate uncertainty in the data, and a slice plane for accurate data value extraction. The parallel coordinates visualization uses specialized brush interactions designed to help users identify nontrivial linear relationships between scalar fields. We describe two novel contributions to parallel coordinates visualizations: linear function brushing and new axis construction. Users have discovered significant relationships among metabolites and anatomy by linking interactions between the three visualizations.

Linked Exploratory Visualizations for Uncertain MR Spectroscopy Data

PubMed Central

Feng, David; Kwock, Lester; Lee, Yueh; Taylor, Russell M.

2010-01-01

We present a system for visualizing magnetic resonance spectroscopy (MRS) data sets. Using MRS, radiologists generate multiple 3D scalar fields of metabolite concentrations within the brain and compare them to anatomical magnetic resonance imaging. By understanding the relationship between metabolic makeup and anatomical structure, radiologists hope to better diagnose and treat tumors and lesions. Our system consists of three linked visualizations: a spatial glyph-based technique we call Scaled Data-Driven Spheres, a parallel coordinates visualization augmented to incorporate uncertainty in the data, and a slice plane for accurate data value extraction. The parallel coordinates visualization uses specialized brush interactions designed to help users identify nontrivial linear relationships between scalar fields. We describe two novel contributions to parallel coordinates visualizations: linear function brushing and new axis construction. Users have discovered significant relationships among metabolites and anatomy by linking interactions between the three visualizations. PMID:21152337

Testing pathways linking exposure to community violence and sexual behaviors among African American youth.

PubMed

Voisin, Dexter R; Hotton, Anna L; Neilands, Torsten B

2014-09-01

Exposure to community violence and HIV sexual risks are two major public health concerns among youth. This study tests various pathways linking exposure to community violence and sexual behaviors among African American adolescents. Using a sample of 563 (61% females) African American youth attending high school we examined whether problematic psychological symptoms, low school engagement, and/or negative perceptions of peer norms about safer sex functioned as pathways linking exposure to community violence and sexual behaviors. Major findings indicated that, for boys, the relationship between exposure to community violence and sexual début and sexual risk behaviors were linked by aggression. In addition, the relationship between exposure to community violence and sexual risk behaviors were linked by negative perceptions of peer attitudes about safer sex. For girls, the relationship between exposure to community violence and sexual début was linked by aggression and negative perceptions of peer attitudes about safer sex. These findings provide support for pathways linking exposure to community violence to sexual behaviors.

Testing Pathways Linking Exposure to Community Violence and Sexual Behaviors Among African American Youth

PubMed Central

Hotton, Anna L.; Neilands, Torsten B.

2014-01-01

Exposure to community violence and HIV sexual risks are two major public health concerns among youth. This study tests various pathways linking exposure to community violence and sexual behaviors among African American adolescents. Using a sample of 563 (61 % females) African American youth attending high school we examined whether problematic psychological symptoms, low school engagement, and/or negative perceptions of peer norms about safer sex functioned as pathways linking exposure to community violence and sexual behaviors. Major findings indicated that, for boys, the relationship between exposure to community violence and sexual début and sexual risk behaviors were linked by aggression. In addition, the relationship between exposure to community violence and sexual risk behaviors were linked by negative perceptions of peer attitudes about safer sex. For girls, the relationship between exposure to community violence and sexual début was linked by aggression and negative perceptions of peer attitudes about safer sex. These findings provide support for pathways linking exposure to community violence to sexual behaviors. PMID:24327295

A new neural framework for visuospatial processing

PubMed Central

Kravitz, Dwight J.; Saleem, Kadharbatcha S.; Baker, Chris I.; Mishkin, Mortimer

2012-01-01

The division of cortical visual processing into distinct dorsal and ventral streams is a key framework that has guided visual neuroscience. The characterization of the ventral stream as a ‘What’ pathway is relatively uncontroversial, but the nature of dorsal stream processing is less clear. Originally proposed as mediating spatial perception (‘Where’), more recent accounts suggest it primarily serves non-conscious visually guided action (‘How’). Here, we identify three pathways emerging from the dorsal stream that consist of projections to the prefrontal and premotor cortices, and a major projection to the medial temporal lobe that courses both directly and indirectly through the posterior cingulate and retrosplenial cortices. These three pathways support both conscious and non-conscious visuospatial processing, including spatial working memory, visually guided action and navigation, respectively. PMID:21415848

Dissociation and Convergence of the Dorsal and Ventral Visual Streams in the Human Prefrontal Cortex

PubMed Central

Takahashi, Emi; Ohki, Kenichi; Kim, Dae-Shik

2012-01-01

Visual information is largely processed through two pathways in the primate brain: an object pathway from the primary visual cortex to the temporal cortex (ventral stream) and a spatial pathway to the parietal cortex (dorsal stream). Whether and to what extent dissociation exists in the human prefrontal cortex (PFC) has long been debated. We examined anatomical connections from functionally defined areas in the temporal and parietal cortices to the PFC, using noninvasive functional and diffusion-weighted magnetic resonance imaging. The right inferior frontal gyrus (IFG) received converging input from both streams, while the right superior frontal gyrus received input only from the dorsal stream. Interstream functional connectivity to the IFG was dynamically recruited only when both object and spatial information were processed. These results suggest that the human PFC receives dissociated and converging visual pathways, and that the right IFG region serves as an integrator of the two types of information. PMID:23063444

Encodings of implied motion for animate and inanimate object categories in the two visual pathways.

PubMed

Lu, Zhengang; Li, Xueting; Meng, Ming

2016-01-15

Previous research has proposed two separate pathways for visual processing: the dorsal pathway for "where" information vs. the ventral pathway for "what" information. Interestingly, the middle temporal cortex (MT) in the dorsal pathway is involved in representing implied motion from still pictures, suggesting an interaction between motion and object related processing. However, the relationship between how the brain encodes implied motion and how the brain encodes object/scene categories is unclear. To address this question, fMRI was used to measure activity along the two pathways corresponding to different animate and inanimate categories of still pictures with different levels of implied motion speed. In the visual areas of both pathways, activity induced by pictures of humans and animals was hardly modulated by the implied motion speed. By contrast, activity in these areas correlated with the implied motion speed for pictures of inanimate objects and scenes. The interaction between implied motion speed and stimuli category was significant, suggesting different encoding mechanisms of implied motion for animate-inanimate distinction. Further multivariate pattern analysis of activity in the dorsal pathway revealed significant effects of stimulus category that are comparable to the ventral pathway. Moreover, still pictures of inanimate objects/scenes with higher implied motion speed evoked activation patterns that were difficult to differentiate from those evoked by pictures of humans and animals, indicating a functional role of implied motion in the representation of object categories. These results provide novel evidence to support integrated encoding of motion and object categories, suggesting a rethink of the relationship between the two visual pathways. Copyright © 2015 Elsevier Inc. All rights reserved.

Designing a Care Pathway Model - A Case Study of the Outpatient Total Hip Arthroplasty Care Pathway.

PubMed

Oosterholt, Robin I; Simonse, Lianne Wl; Boess, Stella U; Vehmeijer, Stephan Bw

2017-03-09

Although the clinical attributes of total hip arthroplasty (THA) care pathways have been thoroughly researched, a detailed understanding of the equally important organisational attributes is still lacking. The aim of this article is to contribute with a model of the outpatient THA care pathway that depicts how the care team should be organised to enable patient discharge on the day of surgery. The outpatient THA care pathway enables patients to be discharged on the day of surgery, shortening the length of stay and intensifying the provision and organisation of care. We utilise visual care modelling to construct a visual design of the organisation of the care pathway. An embedded case study was conducted of the outpatient THA care pathway at a teaching hospital in the Netherlands. The data were collected using a visual care modelling toolkit in 16 semi-structured interviews. Problems and inefficiencies in the care pathway were identified and addressed in the iterative design process. The results are two visual models of the most critical phases of the outpatient THA care pathway: diagnosis & preparation (1) and mobilisation & discharge (4). The results show the care team composition, critical value exchanges, and sequence that enable patient discharge on the day of surgery. The design addressed existing problems and is an optimisation of the case hospital's pathway. The network of actors consists of the patient (1), radiologist (1), anaesthetist (1), nurse specialist (1), pharmacist (1), orthopaedic surgeon (1,4), physiotherapist (1,4), nurse (4), doctor (4) and patient application (1,4). The critical value exchanges include patient preparation (mental and practical), patient education, aligned care team, efficient sequence of value exchanges, early patient mobilisation, flexible availability of the physiotherapist, functional discharge criteria, joint decision making and availability of the care team.

Contrast Responsivity in MT+ Correlates with Phonological Awareness and Reading Measures in Children

PubMed Central

Ben-Shachar, Michal; Dougherty, Robert F.; Deutsch, Gayle K.; Wandell, Brian A.

2007-01-01

There are several independent sets of findings concerning the neural basis of reading. One set demonstrates a powerful relationship between phonological processing and reading skills. Another set reveals a relationship between visual responses in the motion pathways and reading skills. It is widely assumed that these two findings are unrelated. We tested the hypothesis that phonological awareness is related to motion responsivity in children’s MT+. We measured BOLD signals to drifting gratings as a function of contrast. Subjects were 35 children ages 7–12y with a wide range of reading skills. Contrast responsivity in MT+, but not V1, was correlated with phonological awareness and to a lesser extent with two other measures of reading. No correlation was found between MT+ signals and rapid naming, age or general IQ measures. These results establish an important link between visual and phonological processing in children and suggest that MT+ responsivity is a marker for healthy reading development. PMID:17689981

The optic pathway: the development of an eLearning animation.

PubMed

Cooper, Claire; Erolin, Caroline

2018-04-01

The optic pathway is responsible for sending visual information from the eyes to the brain via electrical impulses. It is essential that a sound understanding of this pathway is established in order to determine an accurate diagnosis concerning visual field defects. Although easy for trained neurologists to understand, it is an area which medical students repeatedly struggle to visualise. It is proposed that audio-visual teaching resources can improve students understanding of complex areas of importance. This article describes the development and evaluation of a short animation created for use in the undergraduate neurology curriculum at the University of Dundee School of Medicine.

The Inversion of Sensory Processing by Feedback Pathways: A Model of Visual Cognitive Functions.

ERIC Educational Resources Information Center

Harth, E.; And Others

1987-01-01

Explains the hierarchic structure of the mammalian visual system. Proposes a model in which feedback pathways serve to modify sensory stimuli in ways that enhance and complete sensory input patterns. Investigates the functioning of the system through computer simulations. (ML)

Contralateral Bias of High Spatial Frequency Tuning and Cardinal Direction Selectivity in Mouse Visual Cortex

PubMed Central

Zeitoun, Jack H.; Kim, Hyungtae

2017-01-01

Binocular mechanisms for visual processing are thought to enhance spatial acuity by combining matched input from the two eyes. Studies in the primary visual cortex of carnivores and primates have confirmed that eye-specific neuronal response properties are largely matched. In recent years, the mouse has emerged as a prominent model for binocular visual processing, yet little is known about the spatial frequency tuning of binocular responses in mouse visual cortex. Using calcium imaging in awake mice of both sexes, we show that the spatial frequency preference of cortical responses to the contralateral eye is ∼35% higher than responses to the ipsilateral eye. Furthermore, we find that neurons in binocular visual cortex that respond only to the contralateral eye are tuned to higher spatial frequencies. Binocular neurons that are well matched in spatial frequency preference are also matched in orientation preference. In contrast, we observe that binocularly mismatched cells are more mismatched in orientation tuning. Furthermore, we find that contralateral responses are more direction-selective than ipsilateral responses and are strongly biased to the cardinal directions. The contralateral bias of high spatial frequency tuning was found in both awake and anesthetized recordings. The distinct properties of contralateral cortical responses may reflect the functional segregation of direction-selective, high spatial frequency-preferring neurons in earlier stages of the central visual pathway. Moreover, these results suggest that the development of binocularity and visual acuity may engage distinct circuits in the mouse visual system. SIGNIFICANCE STATEMENT Seeing through two eyes is thought to improve visual acuity by enhancing sensitivity to fine edges. Using calcium imaging of cellular responses in awake mice, we find surprising asymmetries in the spatial processing of eye-specific visual input in binocular primary visual cortex. The contralateral visual pathway is tuned to higher spatial frequencies than the ipsilateral pathway. At the highest spatial frequencies, the contralateral pathway strongly prefers to respond to visual stimuli along the cardinal (horizontal and vertical) axes. These results suggest that monocular, and not binocular, mechanisms set the limit of spatial acuity in mice. Furthermore, they suggest that the development of visual acuity and binocularity in mice involves different circuits. PMID:28924011

Identifying and characterising cerebral visual impairment in children: a review.

PubMed

Philip, Swetha Sara; Dutton, Gordon N

2014-05-01

Cerebral visual impairment (CVI) comprises visual malfunction due to retro-chiasmal visual and visual association pathway pathology. This can be isolated or accompany anterior visual pathway dysfunction. It is a major cause of low vision in children in the developed and developing world due to increasing survival in paediatric and neonatal care. CVI can present in many combinations and degrees. There are multiple causes and it is common in children with cerebral palsy. CVI can be identified easily, if a structured approach to history-taking is employed. This review describes the features of CVI and describes practical management strategies aimed at helping affected children. A literature review was undertaken using 'Medline' and 'Pubmed'. Search terms included cerebral visual impairment, cortical visual impairment, dorsal stream dysfunction and visual function in cerebral palsy. © 2014 The Authors. Clinical and Experimental Optometry © 2014 Optometrists Association Australia.

HPIminer: A text mining system for building and visualizing human protein interaction networks and pathways.

PubMed

Subramani, Suresh; Kalpana, Raja; Monickaraj, Pankaj Moses; Natarajan, Jeyakumar

2015-04-01

The knowledge on protein-protein interactions (PPI) and their related pathways are equally important to understand the biological functions of the living cell. Such information on human proteins is highly desirable to understand the mechanism of several diseases such as cancer, diabetes, and Alzheimer's disease. Because much of that information is buried in biomedical literature, an automated text mining system for visualizing human PPI and pathways is highly desirable. In this paper, we present HPIminer, a text mining system for visualizing human protein interactions and pathways from biomedical literature. HPIminer extracts human PPI information and PPI pairs from biomedical literature, and visualize their associated interactions, networks and pathways using two curated databases HPRD and KEGG. To our knowledge, HPIminer is the first system to build interaction networks from literature as well as curated databases. Further, the new interactions mined only from literature and not reported earlier in databases are highlighted as new. A comparative study with other similar tools shows that the resultant network is more informative and provides additional information on interacting proteins and their associated networks. Copyright © 2015 Elsevier Inc. All rights reserved.

Visual processing in the central bee brain.

PubMed

Paulk, Angelique C; Dacks, Andrew M; Phillips-Portillo, James; Fellous, Jean-Marc; Gronenberg, Wulfila

2009-08-12

Visual scenes comprise enormous amounts of information from which nervous systems extract behaviorally relevant cues. In most model systems, little is known about the transformation of visual information as it occurs along visual pathways. We examined how visual information is transformed physiologically as it is communicated from the eye to higher-order brain centers using bumblebees, which are known for their visual capabilities. We recorded intracellularly in vivo from 30 neurons in the central bumblebee brain (the lateral protocerebrum) and compared these neurons to 132 neurons from more distal areas along the visual pathway, namely the medulla and the lobula. In these three brain regions (medulla, lobula, and central brain), we examined correlations between the neurons' branching patterns and their responses primarily to color, but also to motion stimuli. Visual neurons projecting to the anterior central brain were generally color sensitive, while neurons projecting to the posterior central brain were predominantly motion sensitive. The temporal response properties differed significantly between these areas, with an increase in spike time precision across trials and a decrease in average reliable spiking as visual information processing progressed from the periphery to the central brain. These data suggest that neurons along the visual pathway to the central brain not only are segregated with regard to the physical features of the stimuli (e.g., color and motion), but also differ in the way they encode stimuli, possibly to allow for efficient parallel processing to occur.

Molecular Mechanisms of Diabetic Retinopathy, General Preventive Strategies, and Novel Therapeutic Targets

PubMed Central

Safi, Sher Zaman; Kumar, Selva; Ismail, Ikram Shah Bin

2014-01-01

The growing number of people with diabetes worldwide suggests that diabetic retinopathy (DR) and diabetic macular edema (DME) will continue to be sight threatening factors. The pathogenesis of diabetic retinopathy is a widespread cause of visual impairment in the world and a range of hyperglycemia-linked pathways have been implicated in the initiation and progression of this condition. Despite understanding the polyol pathway flux, activation of protein kinase C (KPC) isoforms, increased hexosamine pathway flux, and increased advanced glycation end-product (AGE) formation, pathogenic mechanisms underlying diabetes induced vision loss are not fully understood. The purpose of this paper is to review molecular mechanisms that regulate cell survival and apoptosis of retinal cells and discuss new and exciting therapeutic targets with comparison to the old and inefficient preventive strategies. This review highlights the recent advancements in understanding hyperglycemia-induced biochemical and molecular alterations, systemic metabolic factors, and aberrant activation of signaling cascades that ultimately lead to activation of a number of transcription factors causing functional and structural damage to retinal cells. It also reviews the established interventions and emerging molecular targets to avert diabetic retinopathy and its associated risk factors. PMID:25105142

Magnocellular pathway for rotation invariant Neocognitron.

PubMed

Ting, C H

1993-03-01

In the mammalian visual system, magnocellular pathway and parvocellular pathway cooperatively process visual information in parallel. The magnocellular pathway is more global and less particular about the details while the parvocellular pathway recognizes objects based on the local features. In many aspects, Neocognitron may be regarded as the artificial analogue of the parvocellular pathway. It is interesting then to model the magnocellular pathway. In order to achieve "rotation invariance" for Neocognitron, we propose a neural network model after the magnocellular pathway and expand its roles to include surmising the orientation of the input pattern prior to recognition. With the incorporation of the magnocellular pathway, a basic shift in the original paradigm has taken place. A pattern is now said to be recognized when and only when one of the winners of the magnocellular pathway is validified by the parvocellular pathway. We have implemented the magnocellular pathway coupled with Neocognitron parallel on transputers; our simulation programme is now able to recognize numerals in arbitrary orientation.

Pathview: an R/Bioconductor package for pathway-based data integration and visualization.

PubMed

Luo, Weijun; Brouwer, Cory

2013-07-15

Pathview is a novel tool set for pathway-based data integration and visualization. It maps and renders user data on relevant pathway graphs. Users only need to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps and integrates user data onto the pathway and renders pathway graphs with the mapped data. Although built as a stand-alone program, Pathview may seamlessly integrate with pathway and functional analysis tools for large-scale and fully automated analysis pipelines. The package is freely available under the GPLv3 license through Bioconductor and R-Forge. It is available at http://bioconductor.org/packages/release/bioc/html/pathview.html and at http://Pathview.r-forge.r-project.org/. luo_weijun@yahoo.com Supplementary data are available at Bioinformatics online.

Seeing More by Showing Less: Orientation-Dependent Transparency Rendering for Fiber Tractography Visualization

PubMed Central

Tax, Chantal M. W.; Chamberland, Maxime; van Stralen, Marijn; Viergever, Max A.; Whittingstall, Kevin; Fortin, David; Descoteaux, Maxime; Leemans, Alexander

2015-01-01

Fiber tractography plays an important role in exploring the architectural organization of fiber trajectories, both in fundamental neuroscience and in clinical applications. With the advent of diffusion MRI (dMRI) approaches that can also model “crossing fibers”, the complexity of the fiber network as reconstructed with tractography has increased tremendously. Many pathways interdigitate and overlap, which hampers an unequivocal 3D visualization of the network and impedes an efficient study of its organization. We propose a novel fiber tractography visualization approach that interactively and selectively adapts the transparency rendering of fiber trajectories as a function of their orientation to enhance the visibility of the spatial context. More specifically, pathways that are oriented (locally or globally) along a user-specified opacity axis can be made more transparent or opaque. This substantially improves the 3D visualization of the fiber network and the exploration of tissue configurations that would otherwise be largely covered by other pathways. We present examples of fiber bundle extraction and neurosurgical planning cases where the added benefit of our new visualization scheme is demonstrated over conventional fiber visualization approaches. PMID:26444010

MOST-visualization: software for producing automated textbook-style maps of genome-scale metabolic networks.

PubMed

Kelley, James J; Maor, Shay; Kim, Min Kyung; Lane, Anatoliy; Lun, Desmond S

2017-08-15

Visualization of metabolites, reactions and pathways in genome-scale metabolic networks (GEMs) can assist in understanding cellular metabolism. Three attributes are desirable in software used for visualizing GEMs: (i) automation, since GEMs can be quite large; (ii) production of understandable maps that provide ease in identification of pathways, reactions and metabolites; and (iii) visualization of the entire network to show how pathways are interconnected. No software currently exists for visualizing GEMs that satisfies all three characteristics, but MOST-Visualization, an extension of the software package MOST (Metabolic Optimization and Simulation Tool), satisfies (i), and by using a pre-drawn overview map of metabolism based on the Roche map satisfies (ii) and comes close to satisfying (iii). MOST is distributed for free on the GNU General Public License. The software and full documentation are available at http://most.ccib.rutgers.edu/. dslun@rutgers.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Magnetic resonance in studies of glaucoma

PubMed Central

Fiedorowicz, Michał; Dyda, Wojciech; Rejdak, Robert; Grieb, Paweł

2011-01-01

Summary Glaucoma is the second leading cause of blindness. It affects retinal ganglion cells and the optic nerve. However, there is emerging evidence that glaucoma also affects other components of the visual pathway and visual cortex. There is a need to employ new methods of in vivo brain evaluation to characterize these changes. Magnetic resonance (MR) techniques are well suited for this purpose. We review data on the MR evaluation of the visual pathway and the use of MR techniques in the study of glaucoma, both in humans and in animal models. These studies demonstrated decreases in optic nerve diameter, localized white matter loss and decrease in visual cortex density. Studies on rats employing manganese-enhanced MRI showed that axonal transport in the optic nerve is affected. Diffusion tensor MRI revealed signs of degeneration of the optic pathway. Functional MRI showed decreased response of the visual cortex after stimulation of the glaucomatous eye. Magnetic resonance spectroscopy demonstrated changes in metabolite levels in the visual cortex in a rat model of glaucoma, although not in glaucoma patients. Further applications of MR techniques in studies of glaucomatous brains are indicated. PMID:21959626

Seeing More by Showing Less: Orientation-Dependent Transparency Rendering for Fiber Tractography Visualization.

PubMed

Tax, Chantal M W; Chamberland, Maxime; van Stralen, Marijn; Viergever, Max A; Whittingstall, Kevin; Fortin, David; Descoteaux, Maxime; Leemans, Alexander

2015-01-01

Fiber tractography plays an important role in exploring the architectural organization of fiber trajectories, both in fundamental neuroscience and in clinical applications. With the advent of diffusion MRI (dMRI) approaches that can also model "crossing fibers", the complexity of the fiber network as reconstructed with tractography has increased tremendously. Many pathways interdigitate and overlap, which hampers an unequivocal 3D visualization of the network and impedes an efficient study of its organization. We propose a novel fiber tractography visualization approach that interactively and selectively adapts the transparency rendering of fiber trajectories as a function of their orientation to enhance the visibility of the spatial context. More specifically, pathways that are oriented (locally or globally) along a user-specified opacity axis can be made more transparent or opaque. This substantially improves the 3D visualization of the fiber network and the exploration of tissue configurations that would otherwise be largely covered by other pathways. We present examples of fiber bundle extraction and neurosurgical planning cases where the added benefit of our new visualization scheme is demonstrated over conventional fiber visualization approaches.

Visual pathway impairment by pituitary adenomas: quantitative diagnostics by diffusion tensor imaging.

PubMed

Lilja, Ylva; Gustafsson, Oscar; Ljungberg, Maria; Starck, Göran; Lindblom, Bertil; Skoglund, Thomas; Bergquist, Henrik; Jakobsson, Karl-Erik; Nilsson, Daniel

2017-09-01

OBJECTIVE Despite ample experience in surgical treatment of pituitary adenomas, little is known about objective indices that may reveal risk of visual impairment caused by tumor growth that leads to compression of the anterior visual pathways. This study aimed to explore diffusion tensor imaging (DTI) as a means for objective assessment of injury to the anterior visual pathways caused by pituitary adenomas. METHODS Twenty-three patients with pituitary adenomas, scheduled for transsphenoidal tumor resection, and 20 healthy control subjects were included in the study. A minimum suprasellar tumor extension of Grade 2-4, according to the SIPAP (suprasellar, infrasellar, parasellar, anterior, and posterior) scale, was required for inclusion. Neuroophthalmological examinations, conventional MRI, and DTI were completed in all subjects and were repeated 6 months after surgery. Quantitative assessment of chiasmal lift, visual field defect (VFD), and DTI parameters from the optic tracts was performed. Linear correlations, group comparisons, and prediction models were done in controls and patients. RESULTS Both the degree of VFD and chiasmal lift were significantly correlated with the radial diffusivity (r = 0.55, p < 0.05 and r = 0.48, p < 0.05, respectively) and the fractional anisotropy (r = -0.58, p < 0.05 and r = -0.47, p < 0.05, respectively) but not with the axial diffusivity. The axial diffusivity differed significantly between controls and patients with VFD, both before and after surgery (p < 0.05); however, no difference was found between patients with and without VFD. Based on the axial diffusivity and fractional anisotropy, a prediction model classified all patients with VFD correctly (sensitivity 1.0), 9 of 12 patients without VFD correctly (sensitivity 0.75), and 17 of 20 controls as controls (specificity 0.85). CONCLUSIONS DTI could detect pathology and degree of injury in the anterior visual pathways that were compressed by pituitary adenomas. The correlation between radial diffusivity and visual impairment may reflect a gradual demyelination in the visual pathways caused by an increased tumor effect. The low level of axial diffusivity found in the patient group may represent early atrophy in the visual pathways, detectable on DTI but not by conventional methods. DTI may provide objective data, detect early signs of injury, and be an additional diagnostic tool for determining indication for surgery in cases of pituitary adenomas.

LinkWinds: An Approach to Visual Data Analysis

NASA Technical Reports Server (NTRS)

Jacobson, Allan S.

1992-01-01

The Linked Windows Interactive Data System (LinkWinds) is a prototype visual data exploration and analysis system resulting from a NASA/JPL program of research into graphical methods for rapidly accessing, displaying and analyzing large multivariate multidisciplinary datasets. It is an integrated multi-application execution environment allowing the dynamic interconnection of multiple windows containing visual displays and/or controls through a data-linking paradigm. This paradigm, which results in a system much like a graphical spreadsheet, is not only a powerful method for organizing large amounts of data for analysis, but provides a highly intuitive, easy to learn user interface on top of the traditional graphical user interface.

Activity in early visual areas predicts interindividual differences in binocular rivalry dynamics

PubMed Central

Yamashiro, Hiroyuki; Mano, Hiroaki; Umeda, Masahiro; Higuchi, Toshihiro; Saiki, Jun

2013-01-01

When dissimilar images are presented to the two eyes, binocular rivalry (BR) occurs, and perception alternates spontaneously between the images. Although neural correlates of the oscillating perception during BR have been found in multiple sites along the visual pathway, the source of BR dynamics is unclear. Psychophysical and modeling studies suggest that both low- and high-level cortical processes underlie BR dynamics. Previous neuroimaging studies have demonstrated the involvement of high-level regions by showing that frontal and parietal cortices responded time locked to spontaneous perceptual alternation in BR. However, a potential contribution of early visual areas to BR dynamics has been overlooked, because these areas also responded to the physical stimulus alternation mimicking BR. In the present study, instead of focusing on activity during perceptual switches, we highlighted brain activity during suppression periods to investigate a potential link between activity in human early visual areas and BR dynamics. We used a strong interocular suppression paradigm called continuous flash suppression to suppress and fluctuate the visibility of a probe stimulus and measured retinotopic responses to the onset of the invisible probe using functional MRI. There were ∼130-fold differences in the median suppression durations across 12 subjects. The individual differences in suppression durations could be predicted by the amplitudes of the retinotopic activity in extrastriate visual areas (V3 and V4v) evoked by the invisible probe. Weaker responses were associated with longer suppression durations. These results demonstrate that retinotopic representations in early visual areas play a role in the dynamics of perceptual alternations during BR. PMID:24353304

Exploring the Link between Visual Perception, Visual-Motor Integration, and Reading in Normal Developing and Impaired Children using DTVP-2.

PubMed

Bellocchi, Stéphanie; Muneaux, Mathilde; Huau, Andréa; Lévêque, Yohana; Jover, Marianne; Ducrot, Stéphanie

2017-08-01

Reading is known to be primarily a linguistic task. However, to successfully decode written words, children also need to develop good visual-perception skills. Furthermore, motor skills are implicated in letter recognition and reading acquisition. Three studies have been designed to determine the link between reading, visual perception, and visual-motor integration using the Developmental Test of Visual Perception version 2 (DTVP-2). Study 1 tests how visual perception and visual-motor integration in kindergarten predict reading outcomes in Grade 1, in typical developing children. Study 2 is aimed at finding out if these skills can be seen as clinical markers in dyslexic children (DD). Study 3 determines if visual-motor integration and motor-reduced visual perception can distinguish DD children according to whether they exhibit or not developmental coordination disorder (DCD). Results showed that phonological awareness and visual-motor integration predicted reading outcomes one year later. DTVP-2 demonstrated similarities and differences in visual-motor integration and motor-reduced visual perception between children with DD, DCD, and both of these deficits. DTVP-2 is a suitable tool to investigate links between visual perception, visual-motor integration and reading, and to differentiate cognitive profiles of children with developmental disabilities (i.e. DD, DCD, and comorbid children). Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

On the usefulness of 'what' and 'where' pathways in vision.

PubMed

de Haan, Edward H F; Cowey, Alan

2011-10-01

The primate visual brain is classically portrayed as a large number of separate 'maps', each dedicated to the processing of specific visual cues, such as colour, motion or faces and their many features. In order to understand this fractionated architecture, the concept of cortical 'pathways' or 'streams' was introduced. In the currently prevailing view, the different maps are organised hierarchically into two major pathways, one involved in recognition and memory (the ventral stream or 'what' pathway) and the other in the programming of action (the dorsal stream or 'where' pathway). In this review, we question this heuristically influential but potentially misleading linear hierarchical pathway model and argue instead for a 'patchwork' or network model. Copyright © 2011 Elsevier Ltd. All rights reserved.

Pathview Web: user friendly pathway visualization and data integration.

PubMed

Luo, Weijun; Pant, Gaurav; Bhavnasi, Yeshvant K; Blanchard, Steven G; Brouwer, Cory

2017-07-03

Pathway analysis is widely used in omics studies. Pathway-based data integration and visualization is a critical component of the analysis. To address this need, we recently developed a novel R package called Pathview. Pathview maps, integrates and renders a large variety of biological data onto molecular pathway graphs. Here we developed the Pathview Web server, as to make pathway visualization and data integration accessible to all scientists, including those without the special computing skills or resources. Pathview Web features an intuitive graphical web interface and a user centered design. The server not only expands the core functions of Pathview, but also provides many useful features not available in the offline R package. Importantly, the server presents a comprehensive workflow for both regular and integrated pathway analysis of multiple omics data. In addition, the server also provides a RESTful API for programmatic access and conveniently integration in third-party software or workflows. Pathview Web is openly and freely accessible at https://pathview.uncc.edu/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Two speed factors of visual recognition independently correlated with fluid intelligence.

PubMed

Tachibana, Ryosuke; Namba, Yuri; Noguchi, Yasuki

2014-01-01

Growing evidence indicates a moderate but significant relationship between processing speed in visuo-cognitive tasks and general intelligence. On the other hand, findings from neuroscience proposed that the primate visual system consists of two major pathways, the ventral pathway for objects recognition and the dorsal pathway for spatial processing and attentive analysis. Previous studies seeking for visuo-cognitive factors of human intelligence indicated a significant correlation between fluid intelligence and the inspection time (IT), an index for a speed of object recognition performed in the ventral pathway. We thus presently examined a possibility that neural processing speed in the dorsal pathway also represented a factor of intelligence. Specifically, we used the mental rotation (MR) task, a popular psychometric measure for mental speed of spatial processing in the dorsal pathway. We found that the speed of MR was significantly correlated with intelligence scores, while it had no correlation with one's IT (recognition speed of visual objects). Our results support the new possibility that intelligence could be explained by two types of mental speed, one related to object recognition (IT) and another for manipulation of mental images (MR).

Human blindsight is mediated by an intact geniculo-extrastriate pathway

PubMed Central

Ajina, Sara; Pestilli, Franco; Rokem, Ariel; Kennard, Christopher; Bridge, Holly

2015-01-01

Although damage to the primary visual cortex (V1) causes hemianopia, many patients retain some residual vision; known as blindsight. We show that blindsight may be facilitated by an intact white-matter pathway between the lateral geniculate nucleus and motion area hMT+. Visual psychophysics, diffusion-weighted magnetic resonance imaging and fibre tractography were applied in 17 patients with V1 damage acquired during adulthood and 9 age-matched controls. Individuals with V1 damage were subdivided into blindsight positive (preserved residual vision) and negative (no residual vision) according to psychophysical performance. All blindsight positive individuals showed intact geniculo-hMT+ pathways, while this pathway was significantly impaired or not measurable in blindsight negative individuals. Two white matter pathways previously implicated in blindsight: (i) superior colliculus to hMT+ and (ii) between hMT+ in each hemisphere were not consistently present in blindsight positive cases. Understanding the visual pathways crucial for residual vision may direct future rehabilitation strategies for hemianopia patients. DOI: http://dx.doi.org/10.7554/eLife.08935.001 PMID:26485034

Real-time Author Co-citation Mapping for Online Searching.

ERIC Educational Resources Information Center

Lin, Xia; White, Howard D.; Buzydlowski, Jan

2003-01-01

Describes the design and implementation of a prototype visualization system, AuthorLink, to enhance author searching. AuthorLink is based on author co-citation analysis and visualization mapping algorithms. AuthorLink produces interactive author maps in real time from a database of 1.26 million records supplied by the Institute for Scientific…

Saccharomyces cerevisiae KTR4, KTR5 and KTR7 encode mannosyltransferases differentially involved in the N- and O-linked glycosylation pathways.

PubMed

Hernández, Nahúm V; López-Ramírez, Luz A; Díaz-Jiménez, Diana F; Mellado-Mojica, Erika; Martínez-Duncker, Iván; López, Mercedes G; Mora-Montes, Héctor M

2017-10-01

Saccharomyces cerevisiae is a model to understand basic aspects of protein glycosylation pathways. Although these metabolic routes have been thoroughly studied, there are still knowledge gaps; among them, the role of the MNT1/KRE2 gene family. This family is composed of nine members, with only six functionally characterized. The enzymes Ktr1, Ktr3, and Mnt1/Kre2 have overlapping activities in both O-linked and N-linked glycan synthesis; while Ktr2 and Yur1 participate exclusively in the elongation of the N-linked glycan outer chain. KTR6 encodes for a phosphomannosyltransferase that synthesizes the cell wall phosphomannan. Here, we aimed to establish the functional role of KTR4, KTR5 and KTR7 in the protein glycosylation pathways, by using heterologous complementation in Candida albicans null mutants lacking members of the MNT1/KRE2 gene family. The three S. cerevisiae genes restored defects in the C. albicans N-linked glycosylation pathway. KTR5 and KTR7 partially complemented a C. albicans null mutant with defects in the synthesis of O-linked glycans, and only KTR4 fully elongated the O-linked glycans like wild-type cells. Therefore, our results suggest that the three genes have a redundant activity in the S. cerevisiae N-linked glycosylation pathway, but KTR4 plays a major role in O-linked glycan synthesis. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Guidance of retinal axons in mammals.

PubMed

Herrera, Eloísa; Erskine, Lynda; Morenilla-Palao, Cruz

2017-11-26

In order to navigate through the surrounding environment many mammals, including humans, primarily rely on vision. The eye, composed of the choroid, sclera, retinal pigmented epithelium, cornea, lens, iris and retina, is the structure that receives the light and converts it into electrical impulses. The retina contains six major types of neurons involving in receiving and modifying visual information and passing it onto higher visual processing centres in the brain. Visual information is relayed to the brain via the axons of retinal ganglion cells (RGCs), a projection known as the optic pathway. The proper formation of this pathway during development is essential for normal vision in the adult individual. Along this pathway there are several points where visual axons face 'choices' in their direction of growth. Understanding how these choices are made has advanced significantly our knowledge of axon guidance mechanisms. Thus, the development of the visual pathway has served as an extremely useful model to reveal general principles of axon pathfinding throughout the nervous system. However, due to its particularities, some cellular and molecular mechanisms are specific for the visual circuit. Here we review both general and specific mechanisms involved in the guidance of mammalian RGC axons when they are traveling from the retina to the brain to establish precise and stereotyped connections that will sustain vision. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dynamic and predictive links between touch and vision.

PubMed

Gray, Rob; Tan, Hong Z

2002-07-01

We investigated crossmodal links between vision and touch for moving objects. In experiment 1, observers discriminated visual targets presented randomly at one of five locations on their forearm. Tactile pulses simulating motion along the forearm preceded visual targets. At short tactile-visual ISIs, discriminations were more rapid when the final tactile pulse and visual target were at the same location. At longer ISIs, discriminations were more rapid when the visual target was offset in the motion direction and were slower for offsets opposite to the motion direction. In experiment 2, speeded tactile discriminations at one of three random locations on the forearm were preceded by a visually simulated approaching object. Discriminations were more rapid when the object approached the location of the tactile stimulation and discrimination performance was dependent on the approaching object's time to contact. These results demonstrate dynamic links in the spatial mapping between vision and touch.

Subliminal spatial cues capture attention and strengthen between-object link.

PubMed

Chou, Wei-Lun; Yeh, Su-Ling

2011-12-01

According to the spreading hypothesis of object-based attention, a subliminal cue that can successfully capture attention to a location within an object should also cause attention to spread throughout the whole cued object and lead to the same-object advantage. Instead, we propose that a subliminal cue favors shifts of attention between objects and strengthens the between-object link, which is coded primarily within the dorsal pathway that governs the visual guidance of action. By adopting the two-rectangle method and using an effective subliminal cue to compare with the classic suprathreshold cue, we found a different result pattern with suprathreshold cues than with subliminal cues. The suprathreshold cue replicated the conventional location and object effects, whereas a subliminal cue led to a different-object advantage with a facilitatory location effect and a same-object advantage with an inhibitory location effect. These results support our consciousness-dependent shifting hypothesis but not the spreading hypothesis. Copyright © 2011 Elsevier Inc. All rights reserved.

An Interactive Platform to Visualize Data-Driven Clinical Pathways for the Management of Multiple Chronic Conditions.

PubMed

Zhang, Yiye; Padman, Rema

2017-01-01

Patients with multiple chronic conditions (MCC) pose an increasingly complex health management challenge worldwide, particularly due to the significant gap in our understanding of how to provide coordinated care. Drawing on our prior research on learning data-driven clinical pathways from actual practice data, this paper describes a prototype, interactive platform for visualizing the pathways of MCC to support shared decision making. Created using Python web framework, JavaScript library and our clinical pathway learning algorithm, the visualization platform allows clinicians and patients to learn the dominant patterns of co-progression of multiple clinical events from their own data, and interactively explore and interpret the pathways. We demonstrate functionalities of the platform using a cluster of 36 patients, identified from a dataset of 1,084 patients, who are diagnosed with at least chronic kidney disease, hypertension, and diabetes. Future evaluation studies will explore the use of this platform to better understand and manage MCC.

Ventral and Dorsal Visual Stream Contributions to the Perception of Object Shape and Object Location

PubMed Central

Zachariou, Valentinos; Klatzky, Roberta; Behrmann, Marlene

2017-01-01

Growing evidence suggests that the functional specialization of the two cortical visual pathways may not be as distinct as originally proposed. Here, we explore possible contributions of the dorsal “where/how” visual stream to shape perception and, conversely, contributions of the ventral “what” visual stream to location perception in human adults. Participants performed a shape detection task and a location detection task while undergoing fMRI. For shape detection, comparable BOLD activation in the ventral and dorsal visual streams was observed, and the magnitude of this activation was correlated with behavioral performance. For location detection, cortical activation was significantly stronger in the dorsal than ventral visual pathway and did not correlate with the behavioral outcome. This asymmetry in cortical profile across tasks is particularly noteworthy given that the visual input was identical and that the tasks were matched for difficulty in performance. We confirmed the asymmetry in a subsequent psychophysical experiment in which participants detected changes in either object location or shape, while ignoring the other, task-irrelevant dimension. Detection of a location change was slowed by an irrelevant shape change matched for difficulty, but the reverse did not hold. We conclude that both ventral and dorsal visual streams contribute to shape perception, but that location processing appears to be essentially a function of the dorsal visual pathway. PMID:24001005

A pathway linking reward circuitry, impulsive sensation-seeking and risky decision-making in young adults: identifying neural markers for new interventions

PubMed Central

Chase, H W; Fournier, J C; Bertocci, M A; Greenberg, T; Aslam, H; Stiffler, R; Lockovich, J; Graur, S; Bebko, G; Forbes, E E; Phillips, M L

2017-01-01

High trait impulsive sensation seeking (ISS) is common in 18–25-year olds, and is associated with risky decision-making and deleterious outcomes. We examined relationships among: activity in reward regions previously associated with ISS during an ISS-relevant context, uncertain reward expectancy (RE), using fMRI; ISS impulsivity and sensation-seeking subcomponents; and risky decision-making in 100, transdiagnostically recruited 18–25-year olds. ISS, anhedonia, anxiety, depression and mania were measured using self-report scales; clinician-administered scales also assessed the latter four. A post-scan risky decision-making task measured ‘risky' (possible win/loss/mixed/neutral) fMRI-task versus ‘sure thing' stimuli. ‘Bias' reflected risky over safe choices. Uncertain RE-related activity in left ventrolateral prefrontal cortex and bilateral ventral striatum was positively associated with an ISS composite score, comprising impulsivity and sensation-seeking–fun-seeking subcomponents (ISSc; P⩽0.001). Bias positively associated with sensation seeking–experience seeking (ES; P=0.003). This relationship was moderated by ISSc (P=0.009): it was evident only in high ISSc individuals. Whole-brain analyses showed a positive relationship between: uncertain RE-related left ventrolateral prefrontal cortical activity and ISSc; uncertain RE-related visual attention and motor preparation neural network activity and ES; and uncertain RE-related dorsal anterior cingulate cortical activity and bias, specifically in high ISSc participants (all ps<0.05, peak-level, family-wise error corrected). We identify an indirect pathway linking greater levels of uncertain RE-related activity in reward, visual attention and motor networks with greater risky decision-making, via positive relationships with impulsivity, fun seeking and ES. These objective neural markers of high ISS can guide new treatment developments for young adults with high levels of this debilitating personality trait. PMID:28418404

Parvocellular Pathway Impairment in Autism Spectrum Disorder: Evidence from Visual Evoked Potentials

ERIC Educational Resources Information Center

Fujita, Takako; Yamasaki, Takao; Kamio, Yoko; Hirose, Shinichi; Tobimatsu, Shozo

2011-01-01

In humans, visual information is processed via parallel channels: the parvocellular (P) pathway analyzes color and form information, whereas the magnocellular (M) stream plays an important role in motion analysis. Individuals with autism spectrum disorder (ASD) often show superior performance in processing fine detail, but impaired performance in…

The large-scale organization of shape processing in the ventral and dorsal pathways

PubMed Central

Culham, Jody C; Plaut, David C; Behrmann, Marlene

2017-01-01

Although shape perception is considered a function of the ventral visual pathway, evidence suggests that the dorsal pathway also derives shape-based representations. In two psychophysics and neuroimaging experiments, we characterized the response properties, topographical organization and perceptual relevance of these representations. In both pathways, shape sensitivity increased from early visual cortex to extrastriate cortex but then decreased in anterior regions. Moreover, the lateral aspect of the ventral pathway and posterior regions of the dorsal pathway were sensitive to the availability of fundamental shape properties, even for unrecognizable images. This apparent representational similarity between the posterior-dorsal and lateral-ventral regions was corroborated by a multivariate analysis. Finally, as with ventral pathway, the activation profile of posterior dorsal regions was correlated with recognition performance, suggesting a possible contribution to perception. These findings challenge a strict functional dichotomy between the pathways and suggest a more distributed model of shape processing. PMID:28980938

Human performance evaluation of a pathway HMD

NASA Astrophysics Data System (ADS)

Lorenz, Bernd; Tobben, Helmut; Schmerwitz, Sven

2005-05-01

Head-up displays (HUD) and helmet (or head)-mounted displays (HMD) aim at reducing the pilot's visual scanning cost in support of concurrent monitoring of both instrument information (near domain) and the outside environment (far domain). An HMD used in combination with a head tracker enables the assessment of the pilot"s head direction in real time allowing symbologies to remain spatially linked to elements of the outside environment. The paper examines the potential added benefits of improved flight path tracking to be expected by displaying symbologies of a virtual 3D perspective pathway plus predictor information on an HMD. Results of a high-fidelity flight-simulation experiment are reported that involved a series of curved approaches supported with such a pathway HMD. The study used a monocular retinal-scanning HMD and involved 18 pilots. Dependent human performance data were derived from flight path tracking measures, subjective measures of mental workload and situation awareness and pilot reactions in response to an unexpected rare event in the outside scene (intruding aircraft on the active runway for the intended landing). Comparison with a standard head-down ILS baseline condition revealed a mix of performance costs and benefits, which is consistent with most of the human factors literature on the general use of HUDs and of HUDs used in combination with pathway guidance: The pathway HMD promoted substantially better flight path tracking but caused also a delayed response to the unexpected event. This effect points to some disadvantages of HUDs referred to as 'attention capture', which may become exaggerated by the additional use of pathway guidance symbology.

Decreased activation along the dorsal visual pathway after a 3-month treatment with galantamine in mild Alzheimer disease: a functional magnetic resonance imaging study.

PubMed

Bokde, Arun L W; Karmann, Michaela; Teipel, Stefan J; Born, Christine; Lieb, Martin; Reiser, Maximilian F; Möller, Hans-Jürgen; Hampel, Harald

2009-04-01

Visual perception has been shown to be altered in Alzheimer disease (AD) patients, and it is associated with decreased cognitive function. Galantamine is an active cholinergic agent, which has been shown to lead to improved cognition in mild to moderate AD patients. This study examined brain activation in a group of mild AD patients after a 3-month open-label treatment with galantamine. The objective was to examine the changes in brain activation due to treatment. There were 2 tasks to visual perception. The first task was a face-matching task to test the activation along the ventral visual pathway, and the second task was a location-matching task to test neuronal function along the dorsal pathway. Brain activation was measured using functional magnetic resonance imaging. There were 5 mild AD patients in the study. There were no differences in the task performance and in the cognitive scores of the Consortium to Establish a Registry for Alzheimer's Disease battery before and after treatment. In the location-matching task, we found a statistically significant decrease in activation along the dorsal visual pathway after galantamine treatment. A previous study found that AD patients had higher activation in the location-matching task compared with healthy controls. There were no differences in activation for the face-matching task after treatment. Our data indicate that treatment with galantamine leads to more efficient visual processing of stimuli or changes the compensatory mechanism in the AD patients. A visual perception task recruiting the dorsal visual system may be useful as a biomarker of treatment effects.

Transient visual pathway critical for normal development of primate grasping behavior.

PubMed

Mundinano, Inaki-Carril; Fox, Dylan M; Kwan, William C; Vidaurre, Diego; Teo, Leon; Homman-Ludiye, Jihane; Goodale, Melvyn A; Leopold, David A; Bourne, James A

2018-02-06

An evolutionary hallmark of anthropoid primates, including humans, is the use of vision to guide precise manual movements. These behaviors are reliant on a specialized visual input to the posterior parietal cortex. Here, we show that normal primate reaching-and-grasping behavior depends critically on a visual pathway through the thalamic pulvinar, which is thought to relay information to the middle temporal (MT) area during early life and then swiftly withdraws. Small MRI-guided lesions to a subdivision of the inferior pulvinar subnucleus (PIm) in the infant marmoset monkey led to permanent deficits in reaching-and-grasping behavior in the adult. This functional loss coincided with the abnormal anatomical development of multiple cortical areas responsible for the guidance of actions. Our study reveals that the transient retino-pulvinar-MT pathway underpins the development of visually guided manual behaviors in primates that are crucial for interacting with complex features in the environment.

Visualizing Internet routing changes.

PubMed

Lad, Mohit; Massey, Dan; Zhang, Lixia

2006-01-01

Today's Internet provides a global data delivery service to millions of end users and routing protocols play a critical role in this service. It is important to be able to identify and diagnose any problems occurring in Internet routing. However, the Internet's sheer size makes this task difficult. One cannot easily extract out the most important or relevant routing information from the large amounts of data collected from multiple routers. To tackle this problem, we have developed Link-Rank, a tool to visualize Internet routing changes at the global scale. Link-Rank weighs links in a topological graph by the number of routes carried over each link and visually captures changes in link weights in the form of a topological graph with adjustable size. Using Link-Rank, network operators can easily observe important routing changes from massive amounts of routing data, discover otherwise unnoticed routing problems, understand the impact of topological events, and infer root causes of observed routing changes.

Imaging anatomy of the vestibular and visual systems.

PubMed

Gunny, Roxana; Yousry, Tarek A

2007-02-01

This review will outline the imaging anatomy of the vestibular and visual pathways, using computed tomography and magnetic resonance imaging, with emphasis on the more recent developments in neuroimaging. Technical advances in computed tomography and magnetic resonance imaging, such as the advent of multislice computed tomography and newer magnetic resonance imaging techniques such as T2-weighted magnetic resonance cisternography, have improved the imaging of the vestibular and visual pathways, allowing better visualization of the end organs and peripheral nerves. Higher field strength magnetic resonance imaging is a promising tool, which has been used to evaluate and resolve fine anatomic detail in vitro, as in the labyrinth. Advanced magnetic resonance imaging techniques such as functional magnetic resonance imaging and diffusion tractography have been used to identify cortical areas of activation and associated white matter pathways, and show potential for the future identification of complex neuronal relays involved in integrating these pathways. The assessment of the various components of the vestibular and the visual systems has improved with more detailed research on the imaging anatomy of these systems, the advent of high field magnetic resonance scanners and multislice computerized tomography, and the wider use of specific techniques such as tractography which displays white matter tracts not directly accessible until now.

Integrated pathway-based transcription regulation network mining and visualization based on gene expression profiles.

PubMed

Kibinge, Nelson; Ono, Naoaki; Horie, Masafumi; Sato, Tetsuo; Sugiura, Tadao; Altaf-Ul-Amin, Md; Saito, Akira; Kanaya, Shigehiko

2016-06-01

Conventionally, workflows examining transcription regulation networks from gene expression data involve distinct analytical steps. There is a need for pipelines that unify data mining and inference deduction into a singular framework to enhance interpretation and hypotheses generation. We propose a workflow that merges network construction with gene expression data mining focusing on regulation processes in the context of transcription factor driven gene regulation. The pipeline implements pathway-based modularization of expression profiles into functional units to improve biological interpretation. The integrated workflow was implemented as a web application software (TransReguloNet) with functions that enable pathway visualization and comparison of transcription factor activity between sample conditions defined in the experimental design. The pipeline merges differential expression, network construction, pathway-based abstraction, clustering and visualization. The framework was applied in analysis of actual expression datasets related to lung, breast and prostrate cancer. Copyright © 2016 Elsevier Inc. All rights reserved.

R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

PubMed Central

Kramer, Frank; Bayerlová, Michaela; Beißbarth, Tim

2014-01-01

Putting new findings into the context of available literature knowledge is one approach to deal with the surge of high-throughput data results. Furthermore, prior knowledge can increase the performance and stability of bioinformatic algorithms, for example, methods for network reconstruction. In this review, we examine software packages for the statistical computing framework R, which enable the integration of pathway data for further bioinformatic analyses. Different approaches to integrate and visualize pathway data are identified and packages are stratified concerning their features according to a number of different aspects: data import strategies, the extent of available data, dependencies on external tools, integration with further analysis steps and visualization options are considered. A total of 12 packages integrating pathway data are reviewed in this manuscript. These are supplemented by five R-specific packages for visualization and six connector packages, which provide access to external tools. PMID:24833336

Orbital complications:diagnosis of different rhinological causes.

PubMed

Matsuba, Yumiko; Strassen, Ulrich; Hofauer, Benedikt; Bas, Murat; Knopf, Andreas

2015-09-01

To evaluate the clinical course of orbital complication using a standardised diagnostic pathway. Seventy-three patients with orbital complications underwent a multimodal diagnostic pathway comprising ENT examination, leucocytes/CRP, CT-/MRI-scanning and disease-related data. Twenty-nine patients suffered from rhinosinusitis, 28 from mucoceles, 13 patients from neoplasms and three patients from rheumatic disorders. Clinical examination diagnosed 60 patients with eyelid swelling, 55 patients with ocular pain, 14 patients with diplopia, 4 patients with exophthalmus, 29 patients with visual field defect and 4 patients with visual loss. The diagnostic pathway identified acute rhinosinusitis with a sensitivity/specificity of 90 %/90 %, mucoceles with 79 %/100 %, neoplasms with 100 %/96 % and granulomatosis with polyangiitis with 100 %/100 %, respectively. All patients left the hospital in good general condition and with regular ocular motility; two patients suffered persistent visual loss. The standardised application of a widely accepted diagnostic pathway reliably distinguishes different causes of orbital complication.

Maternal education and child nutritional status in Bolivia: finding the links.

PubMed

Frost, Michelle Bellessa; Forste, Renata; Haas, David W

2005-01-01

This study models various pathways linking maternal education and child nutritional status in Bolivia, using a national sample of children. Pathways examined include socioeconomic status, health knowledge, modern attitudes towards health care, female autonomy, and reproductive behavior. The data come from the 1998 Bolivia Demographic and Health Survey. Logistic regression results suggest that socioeconomic factors are the most important pathways linking maternal education and child nutritional status, and that modern attitudes about health care also explain the impact of education. Health care knowledge accounts for less of the effect of maternal education on child nutritional status, with autonomy being the weakest pathway. Other pathways, such as reproductive behaviors, appear to influence nutritional status independent of maternal education. Overall, the pathways examined accounted for 60 percent of the effect of maternal education on child nutritional status.

Dynamic interactions between visual working memory and saccade target selection

PubMed Central

Schneegans, Sebastian; Spencer, John P.; Schöner, Gregor; Hwang, Seongmin; Hollingworth, Andrew

2014-01-01

Recent psychophysical experiments have shown that working memory for visual surface features interacts with saccadic motor planning, even in tasks where the saccade target is unambiguously specified by spatial cues. Specifically, a match between a memorized color and the color of either the designated target or a distractor stimulus influences saccade target selection, saccade amplitudes, and latencies in a systematic fashion. To elucidate these effects, we present a dynamic neural field model in combination with new experimental data. The model captures the neural processes underlying visual perception, working memory, and saccade planning relevant to the psychophysical experiment. It consists of a low-level visual sensory representation that interacts with two separate pathways: a spatial pathway implementing spatial attention and saccade generation, and a surface feature pathway implementing color working memory and feature attention. Due to bidirectional coupling between visual working memory and feature attention in the model, the working memory content can indirectly exert an effect on perceptual processing in the low-level sensory representation. This in turn biases saccadic movement planning in the spatial pathway, allowing the model to quantitatively reproduce the observed interaction effects. The continuous coupling between representations in the model also implies that modulation should be bidirectional, and model simulations provide specific predictions for complementary effects of saccade target selection on visual working memory. These predictions were empirically confirmed in a new experiment: Memory for a sample color was biased toward the color of a task-irrelevant saccade target object, demonstrating the bidirectional coupling between visual working memory and perceptual processing. PMID:25228628

Designing a Care Pathway Model – A Case Study of the Outpatient Total Hip Arthroplasty Care Pathway

PubMed Central

Oosterholt, Robin I; Boess, Stella U; Vehmeijer, Stephan BW

2017-01-01

Introduction: Although the clinical attributes of total hip arthroplasty (THA) care pathways have been thoroughly researched, a detailed understanding of the equally important organisational attributes is still lacking. The aim of this article is to contribute with a model of the outpatient THA care pathway that depicts how the care team should be organised to enable patient discharge on the day of surgery. Theory: The outpatient THA care pathway enables patients to be discharged on the day of surgery, shortening the length of stay and intensifying the provision and organisation of care. We utilise visual care modelling to construct a visual design of the organisation of the care pathway. Methods: An embedded case study was conducted of the outpatient THA care pathway at a teaching hospital in the Netherlands. The data were collected using a visual care modelling toolkit in 16 semi-structured interviews. Problems and inefficiencies in the care pathway were identified and addressed in the iterative design process. Results: The results are two visual models of the most critical phases of the outpatient THA care pathway: diagnosis & preparation (1) and mobilisation & discharge (4). The results show the care team composition, critical value exchanges, and sequence that enable patient discharge on the day of surgery. Conclusion: The design addressed existing problems and is an optimisation of the case hospital’s pathway. The network of actors consists of the patient (1), radiologist (1), anaesthetist (1), nurse specialist (1), pharmacist (1), orthopaedic surgeon (1,4), physiotherapist (1,4), nurse (4), doctor (4) and patient application (1,4). The critical value exchanges include patient preparation (mental and practical), patient education, aligned care team, efficient sequence of value exchanges, early patient mobilisation, flexible availability of the physiotherapist, functional discharge criteria, joint decision making and availability of the care team. PMID:29042844

Parallel processing of general and specific threat during early stages of perception

PubMed Central

2016-01-01

Differential processing of threat can consummate as early as 100 ms post-stimulus. Moreover, early perception not only differentiates threat from non-threat stimuli but also distinguishes among discrete threat subtypes (e.g. fear, disgust and anger). Combining spatial-frequency-filtered images of fear, disgust and neutral scenes with high-density event-related potentials and intracranial source estimation, we investigated the neural underpinnings of general and specific threat processing in early stages of perception. Conveyed in low spatial frequencies, fear and disgust images evoked convergent visual responses with similarly enhanced N1 potentials and dorsal visual (middle temporal gyrus) cortical activity (relative to neutral cues; peaking at 156 ms). Nevertheless, conveyed in high spatial frequencies, fear and disgust elicited divergent visual responses, with fear enhancing and disgust suppressing P1 potentials and ventral visual (occipital fusiform) cortical activity (peaking at 121 ms). Therefore, general and specific threat processing operates in parallel in early perception, with the ventral visual pathway engaged in specific processing of discrete threats and the dorsal visual pathway in general threat processing. Furthermore, selectively tuned to distinctive spatial-frequency channels and visual pathways, these parallel processes underpin dimensional and categorical threat characterization, promoting efficient threat response. These findings thus lend support to hybrid models of emotion. PMID:26412811

YMDB 2.0: a significantly expanded version of the yeast metabolome database.

PubMed

Ramirez-Gaona, Miguel; Marcu, Ana; Pon, Allison; Guo, An Chi; Sajed, Tanvir; Wishart, Noah A; Karu, Naama; Djoumbou Feunang, Yannick; Arndt, David; Wishart, David S

2017-01-04

YMDB or the Yeast Metabolome Database (http://www.ymdb.ca/) is a comprehensive database containing extensive information on the genome and metabolome of Saccharomyces cerevisiae Initially released in 2012, the YMDB has gone through a significant expansion and a number of improvements over the past 4 years. This manuscript describes the most recent version of YMDB (YMDB 2.0). More specifically, it provides an updated description of the database that was previously described in the 2012 NAR Database Issue and it details many of the additions and improvements made to the YMDB over that time. Some of the most important changes include a 7-fold increase in the number of compounds in the database (from 2007 to 16 042), a 430-fold increase in the number of metabolic and signaling pathway diagrams (from 66 to 28 734), a 16-fold increase in the number of compounds linked to pathways (from 742 to 12 733), a 17-fold increase in the numbers of compounds with nuclear magnetic resonance or MS spectra (from 783 to 13 173) and an increase in both the number of data fields and the number of links to external databases. In addition to these database expansions, a number of improvements to YMDB's web interface and its data visualization tools have been made. These additions and improvements should greatly improve the ease, the speed and the quantity of data that can be extracted, searched or viewed within YMDB. Overall, we believe these improvements should not only improve the understanding of the metabolism of S. cerevisiae, but also allow more in-depth exploration of its extensive metabolic networks, signaling pathways and biochemistry. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Functional Dissociations within the Ventral Object Processing Pathway: Cognitive Modules or a Hierarchical Continuum?

ERIC Educational Resources Information Center

Cowell, Rosemary A.; Bussey, Timothy J.; Saksida, Lisa M.

2010-01-01

We examined the organization and function of the ventral object processing pathway. The prevailing theoretical approach in this field holds that the ventral object processing stream has a modular organization, in which visual perception is carried out in posterior regions and visual memory is carried out, independently, in the anterior temporal…

Improving Dorsal Stream Function in Dyslexics by Training Figure/Ground Motion Discrimination Improves Attention, Reading Fluency, and Working Memory.

PubMed

Lawton, Teri

2016-01-01

There is an ongoing debate about whether the cause of dyslexia is based on linguistic, auditory, or visual timing deficits. To investigate this issue three interventions were compared in 58 dyslexics in second grade (7 years on average), two targeting the temporal dynamics (timing) of either the auditory or visual pathways with a third reading intervention (control group) targeting linguistic word building. Visual pathway training in dyslexics to improve direction-discrimination of moving test patterns relative to a stationary background (figure/ground discrimination) significantly improved attention, reading fluency, both speed and comprehension, phonological processing, and both auditory and visual working memory relative to controls, whereas auditory training to improve phonological processing did not improve these academic skills significantly more than found for controls. This study supports the hypothesis that faulty timing in synchronizing the activity of magnocellular with parvocellular visual pathways is a fundamental cause of dyslexia, and argues against the assumption that reading deficiencies in dyslexia are caused by phonological deficits. This study demonstrates that visual movement direction-discrimination can be used to not only detect dyslexia early, but also for its successful treatment, so that reading problems do not prevent children from readily learning.

A Web Tool for Generating High Quality Machine-readable Biological Pathways.

PubMed

Ramirez-Gaona, Miguel; Marcu, Ana; Pon, Allison; Grant, Jason; Wu, Anthony; Wishart, David S

2017-02-08

PathWhiz is a web server built to facilitate the creation of colorful, interactive, visually pleasing pathway diagrams that are rich in biological information. The pathways generated by this online application are machine-readable and fully compatible with essentially all web-browsers and computer operating systems. It uses a specially developed, web-enabled pathway drawing interface that permits the selection and placement of different combinations of pre-drawn biological or biochemical entities to depict reactions, interactions, transport processes and binding events. This palette of entities consists of chemical compounds, proteins, nucleic acids, cellular membranes, subcellular structures, tissues, and organs. All of the visual elements in it can be interactively adjusted and customized. Furthermore, because this tool is a web server, all pathways and pathway elements are publicly accessible. This kind of pathway "crowd sourcing" means that PathWhiz already contains a large and rapidly growing collection of previously drawn pathways and pathway elements. Here we describe a protocol for the quick and easy creation of new pathways and the alteration of existing pathways. To further facilitate pathway editing and creation, the tool contains replication and propagation functions. The replication function allows existing pathways to be used as templates to create or edit new pathways. The propagation function allows one to take an existing pathway and automatically propagate it across different species. Pathways created with this tool can be "re-styled" into different formats (KEGG-like or text-book like), colored with different backgrounds, exported to BioPAX, SBGN-ML, SBML, or PWML data exchange formats, and downloaded as PNG or SVG images. The pathways can easily be incorporated into online databases, integrated into presentations, posters or publications, or used exclusively for online visualization and exploration. This protocol has been successfully applied to generate over 2,000 pathway diagrams, which are now found in many online databases including HMDB, DrugBank, SMPDB, and ECMDB.

Equitable Access by Design. A Conceptual Framework for Integrated Student Supports within Linked Learning Pathways

ERIC Educational Resources Information Center

de Velasco, Jorge Ruiz; Newman, Elizabeth; Borsato, Graciela

2016-01-01

This report proposes a conceptual framework for defining and implementing a system of integrated student supports that provides equitable access to college and career readiness via Linked Learning pathways in high schools. The framework emphasizes the central commitment of the Linked Learning approach to challenge prevailing norms of…

Building Data-Driven Pathways From Routinely Collected Hospital Data: A Case Study on Prostate Cancer

PubMed Central

Clark, Jeremy; Cooper, Colin S; Mills, Robert; Rayward-Smith, Victor J; de la Iglesia, Beatriz

2015-01-01

Background Routinely collected data in hospitals is complex, typically heterogeneous, and scattered across multiple Hospital Information Systems (HIS). This big data, created as a byproduct of health care activities, has the potential to provide a better understanding of diseases, unearth hidden patterns, and improve services and cost. The extent and uses of such data rely on its quality, which is not consistently checked, nor fully understood. Nevertheless, using routine data for the construction of data-driven clinical pathways, describing processes and trends, is a key topic receiving increasing attention in the literature. Traditional algorithms do not cope well with unstructured processes or data, and do not produce clinically meaningful visualizations. Supporting systems that provide additional information, context, and quality assurance inspection are needed. Objective The objective of the study is to explore how routine hospital data can be used to develop data-driven pathways that describe the journeys that patients take through care, and their potential uses in biomedical research; it proposes a framework for the construction, quality assessment, and visualization of patient pathways for clinical studies and decision support using a case study on prostate cancer. Methods Data pertaining to prostate cancer patients were extracted from a large UK hospital from eight different HIS, validated, and complemented with information from the local cancer registry. Data-driven pathways were built for each of the 1904 patients and an expert knowledge base, containing rules on the prostate cancer biomarker, was used to assess the completeness and utility of the pathways for a specific clinical study. Software components were built to provide meaningful visualizations for the constructed pathways. Results The proposed framework and pathway formalism enable the summarization, visualization, and querying of complex patient-centric clinical information, as well as the computation of quality indicators and dimensions. A novel graphical representation of the pathways allows the synthesis of such information. Conclusions Clinical pathways built from routinely collected hospital data can unearth information about patients and diseases that may otherwise be unavailable or overlooked in hospitals. Data-driven clinical pathways allow for heterogeneous data (ie, semistructured and unstructured data) to be collated over a unified data model and for data quality dimensions to be assessed. This work has enabled further research on prostate cancer and its biomarkers, and on the development and application of methods to mine, compare, analyze, and visualize pathways constructed from routine data. This is an important development for the reuse of big data in hospitals. PMID:26162314

Two Speed Factors of Visual Recognition Independently Correlated with Fluid Intelligence

PubMed Central

Tachibana, Ryosuke; Namba, Yuri; Noguchi, Yasuki

2014-01-01

Growing evidence indicates a moderate but significant relationship between processing speed in visuo-cognitive tasks and general intelligence. On the other hand, findings from neuroscience proposed that the primate visual system consists of two major pathways, the ventral pathway for objects recognition and the dorsal pathway for spatial processing and attentive analysis. Previous studies seeking for visuo-cognitive factors of human intelligence indicated a significant correlation between fluid intelligence and the inspection time (IT), an index for a speed of object recognition performed in the ventral pathway. We thus presently examined a possibility that neural processing speed in the dorsal pathway also represented a factor of intelligence. Specifically, we used the mental rotation (MR) task, a popular psychometric measure for mental speed of spatial processing in the dorsal pathway. We found that the speed of MR was significantly correlated with intelligence scores, while it had no correlation with one’s IT (recognition speed of visual objects). Our results support the new possibility that intelligence could be explained by two types of mental speed, one related to object recognition (IT) and another for manipulation of mental images (MR). PMID:24825574

Lack of Multisensory Integration in Hemianopia: No Influence of Visual Stimuli on Aurally Guided Saccades to the Blind Hemifield

PubMed Central

Ten Brink, Antonia F.; Nijboer, Tanja C. W.; Bergsma, Douwe P.; Barton, Jason J. S.; Van der Stigchel, Stefan

2015-01-01

In patients with visual hemifield defects residual visual functions may be present, a phenomenon called blindsight. The superior colliculus (SC) is part of the spared pathway that is considered to be responsible for this phenomenon. Given that the SC processes input from different modalities and is involved in the programming of saccadic eye movements, the aim of the present study was to examine whether multimodal integration can modulate oculomotor competition in the damaged hemifield. We conducted two experiments with eight patients who had visual field defects due to lesions that affected the retinogeniculate pathway but spared the retinotectal direct SC pathway. They had to make saccades to an auditory target that was presented alone or in combination with a visual stimulus. The visual stimulus could either be spatially coincident with the auditory target (possibly enhancing the auditory target signal), or spatially disparate to the auditory target (possibly competing with the auditory tar-get signal). For each patient we compared the saccade endpoint deviation in these two bi-modal conditions with the endpoint deviation in the unimodal condition (auditory target alone). In all seven hemianopic patients, saccade accuracy was affected only by visual stimuli in the intact, but not in the blind visual field. In one patient with a more limited quadrantano-pia, a facilitation effect of the spatially coincident visual stimulus was observed. We conclude that our results show that multisensory integration is infrequent in the blind field of patients with hemianopia. PMID:25835952

Node, Node-Link, and Node-Link-Group Diagrams: An Evaluation.

PubMed

Saket, Bahador; Simonetto, Paolo; Kobourov, Stephen; Börner, Katy

2014-12-01

Effectively showing the relationships between objects in a dataset is one of the main tasks in information visualization. Typically there is a well-defined notion of distance between pairs of objects, and traditional approaches such as principal component analysis or multi-dimensional scaling are used to place the objects as points in 2D space, so that similar objects are close to each other. In another typical setting, the dataset is visualized as a network graph, where related nodes are connected by links. More recently, datasets are also visualized as maps, where in addition to nodes and links, there is an explicit representation of groups and clusters. We consider these three Techniques, characterized by a progressive increase of the amount of encoded information: node diagrams, node-link diagrams and node-link-group diagrams. We assess these three types of diagrams with a controlled experiment that covers nine different tasks falling broadly in three categories: node-based tasks, network-based tasks and group-based tasks. Our findings indicate that adding links, or links and group representations, does not negatively impact performance (time and accuracy) of node-based tasks. Similarly, adding group representations does not negatively impact the performance of network-based tasks. Node-link-group diagrams outperform the others on group-based tasks. These conclusions contradict results in other studies, in similar but subtly different settings. Taken together, however, such results can have significant implications for the design of standard and domain snecific visualizations tools.

Escape from harm: linking affective vision and motor responses during active avoidance

PubMed Central

Keil, Andreas

2014-01-01

When organisms confront unpleasant objects in their natural environments, they engage in behaviors that allow them to avoid aversive outcomes. Here, we linked visual processing of threat to its behavioral consequences by including a motor response that terminated exposure to an aversive event. Dense-array steady-state visual evoked potentials were recorded in response to conditioned threat and safety signals viewed in active or passive behavioral contexts. The amplitude of neuronal responses in visual cortex increased additively, as a function of emotional value and action relevance. The gain in local cortical population activity for threat relative to safety cues persisted when aversive reinforcement was behaviorally terminated, suggesting a lingering emotionally based response amplification within the visual system. Distinct patterns of long-range neural synchrony emerged between the visual cortex and extravisual regions. Increased coupling between visual and higher-order structures was observed specifically during active perception of threat, consistent with a reorganization of neuronal populations involved in linking sensory processing to action preparation. PMID:24493849

Applications of Optical Coherence Tomography in Pediatric Clinical Neuroscience

PubMed Central

Avery, Robert A.; Rajjoub, Raneem D.; Trimboli-Heidler, Carmelina; Waldman, Amy T.

2015-01-01

For nearly two centuries, the ophthalmoscope has permitted examination of the retina and optic nerve—the only axons directly visualized by the physician. The retinal ganglion cells project their axons, which travel along the innermost retina to form the optic nerve, marking the beginning of the anterior visual pathway. Both the structure and function of the visual pathway are essential components of the neurologic examination as it can be involved in numerous acquired, congenital and genetic central nervous system conditions. The development of optical coherence tomography now permits the pediatric neuroscientist to visualize and quantify the optic nerve and retinal layers with unprecedented resolution. As optical coherence tomography becomes more accessible and integrated into research and clinical care, the pediatric neuroscientist may have the opportunity to utilize and/or interpret results from this device. This review describes the basic technical features of optical coherence tomography and highlights its potential clinical and research applications in pediatric clinical neuroscience including optic nerve swelling, optic neuritis, tumors of the visual pathway, vigabatrin toxicity, nystagmus, and neurodegenerative conditions. PMID:25803824

Applications of optical coherence tomography in pediatric clinical neuroscience.

PubMed

Avery, Robert A; Rajjoub, Raneem D; Trimboli-Heidler, Carmelina; Waldman, Amy T

2015-04-01

For nearly two centuries, the ophthalmoscope has permitted examination of the retina and optic nerve-the only axons directly visualized by the physician. The retinal ganglion cells project their axons, which travel along the innermost retina to form the optic nerve, marking the beginning of the anterior visual pathway. Both the structure and function of the visual pathway are essential components of the neurologic examination as it can be involved in numerous acquired, congenital and genetic central nervous system conditions. The development of optical coherence tomography now permits the pediatric neuroscientist to visualize and quantify the optic nerve and retinal layers with unprecedented resolution. As optical coherence tomography becomes more accessible and integrated into research and clinical care, the pediatric neuroscientist may have the opportunity to utilize and/or interpret results from this device. This review describes the basic technical features of optical coherence tomography and highlights its potential clinical and research applications in pediatric clinical neuroscience including optic nerve swelling, optic neuritis, tumors of the visual pathway, vigabatrin toxicity, nystagmus, and neurodegenerative conditions. Georg Thieme Verlag KG Stuttgart · New York.

Dissociating 'what' and 'how' in visual form agnosia: a computational investigation.

PubMed

Vecera, S P

2002-01-01

Patients with visual form agnosia exhibit a profound impairment in shape perception (what an object is) coupled with intact visuomotor functions (how to act on an object), demonstrating a dissociation between visual perception and action. How can these patients act on objects that they cannot perceive? Although two explanations of this 'what-how' dissociation have been offered, each explanation has shortcomings. A 'pathway information' account of the 'what-how' dissociation is presented in this paper. This account hypothesizes that 'where' and 'how' tasks require less information than 'what' tasks, thereby allowing 'where/how' to remain relatively spared in the face of neurological damage. Simulations with a neural network model test the predictions of the pathway information account. Following damage to an input layer common to the 'what' and 'where/how' pathways, the model performs object identification more poorly than spatial localization. Thus, the model offers a parsimonious explanation of differential 'what-how' performance in visual form agnosia. The simulation results are discussed in terms of their implications for visual form agnosia and other neuropsychological syndromes.

DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site.

PubMed

Kearney, Bradley M; Johnson, Christian W; Roberts, Daniel M; Swartz, Paul; Mattos, Carla

2014-02-06

Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleotide-dependent manner. Here we present the program Detection of Related Solvent Positions (DRoP) for crystallographic water analysis on protein surfaces and use it to study Ras. DRoP reads and superimposes multiple Protein Data Bank coordinates, transfers symmetry-related water molecules to the position closest to the protein surface, and ranks the waters according to how well conserved and tightly clustered they are in the set of structures. Coloring according to this rank allows visualization of the results. The effector-binding region of Ras is hydrated with highly conserved water molecules at the interface between the P-loop, switch I, and switch II, as well as at the Raf-RBD binding pocket. Furthermore, we discovered a new conserved water-mediated H-bonding network present in Ras-GTP, but not in Ras-GDP, that links the nucleotide sensor residues R161 and R164 on helix 5 to the active site. The double mutant RasN85A/N86A, where the final link between helix 5 and the nucleotide is not possible, is a severely impaired enzyme, while the single mutant RasN86A, with partial connection to the active site, has a wild-type hydrolysis rate. DRoP was instrumental in determining the water-mediated connectivity networks that link two lobes of the catalytic domain in Ras. Copyright © 2013 Elsevier Ltd. All rights reserved.

Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis

NASA Astrophysics Data System (ADS)

Bartell, Jennifer A.; Blazier, Anna S.; Yen, Phillip; Thøgersen, Juliane C.; Jelsbak, Lars; Goldberg, Joanna B.; Papin, Jason A.

2017-03-01

Virulence-linked pathways in opportunistic pathogens are putative therapeutic targets that may be associated with less potential for resistance than targets in growth-essential pathways. However, efficacy of virulence-linked targets may be affected by the contribution of virulence-related genes to metabolism. We evaluate the complex interrelationships between growth and virulence-linked pathways using a genome-scale metabolic network reconstruction of Pseudomonas aeruginosa strain PA14 and an updated, expanded reconstruction of P. aeruginosa strain PAO1. The PA14 reconstruction accounts for the activity of 112 virulence-linked genes and virulence factor synthesis pathways that produce 17 unique compounds. We integrate eight published genome-scale mutant screens to validate gene essentiality predictions in rich media, contextualize intra-screen discrepancies and evaluate virulence-linked gene distribution across essentiality datasets. Computational screening further elucidates interconnectivity between inhibition of virulence factor synthesis and growth. Successful validation of selected gene perturbations using PA14 transposon mutants demonstrates the utility of model-driven screening of therapeutic targets.

Objective assessment of chromatic and achromatic pattern adaptation reveals the temporal response properties of different visual pathways.

PubMed

Robson, Anthony G; Kulikowski, Janus J

2012-11-01

The aim was to investigate the temporal response properties of magnocellular, parvocellular, and koniocellular visual pathways using increment/decrement changes in contrast to elicit visual evoked potentials (VEPs). Static achromatic and isoluminant chromatic gratings were generated on a monitor. Chromatic gratings were modulated along red/green (R/G) or subject-specific tritanopic confusion axes, established using a minimum distinct border criterion. Isoluminance was determined using minimum flicker photometry. Achromatic and chromatic VEPs were recorded to contrast increments and decrements of 0.1 or 0.2 superimposed on the static gratings (masking contrast 0-0.6). Achromatic increment/decrement changes in contrast evoked a percept of apparent motion when the spatial frequency was low; VEPs to such stimuli were positive in polarity and largely unaffected by high levels of static contrast, consistent with transient response mechanisms. VEPs to finer achromatic gratings showed marked attenuation as static contrast was increased. Chromatic VEPs to R/G or tritan chromatic contrast increments were of negative polarity and showed progressive attenuation as static contrast was increased, in keeping with increasing desensitization of the sustained responses of the color-opponent visual pathways. Chromatic contrast decrement VEPs were of positive polarity and less sensitive to pattern adaptation. The relative contribution of sustained/transient mechanisms to achromatic processing is spatial frequency dependent. Chromatic contrast increment VEPs reflect the sustained temporal response properties of parvocellular and koniocellular pathways. Cortical VEPs can provide an objective measure of pattern adaptation and can be used to probe the temporal response characteristics of different visual pathways.

Integrating Mechanisms for Insulin Resistance: Common Threads and Missing Links

PubMed Central

Samuel, Varman T.; Shulman, Gerald I.

2012-01-01

Insulin resistance is a complex metabolic disorder that defies a single etiological pathway. Accumulation of ectopic lipid metabolites, activation of the unfolded protein response (UPR) pathway and innate immune pathways have all been implicated in the pathogenesis of insulin resistance. However, these pathways are also closely linked to changes in fatty acid uptake, lipogenesis, and energy expenditure that can impact ectopic lipid deposition. Ultimately, accumulation of specific lipid metabolites (diacylglycerols and/or ceramides) in liver and skeletal muscle, may be a common pathway leading to impaired insulin signaling and insulin resistance. PMID:22385956

Stimulation of the Lateral Geniculate, Superior Colliculus, or Visual Cortex is Sufficient for Eyeblink Conditioning in Rats

ERIC Educational Resources Information Center

Halverson, Hunter E.; Hubbard, Erin M.; Freeman, John H.

2009-01-01

The role of the cerebellum in eyeblink conditioning is well established. Less work has been done to identify the necessary conditioned stimulus (CS) pathways that project sensory information to the cerebellum. A possible visual CS pathway has been hypothesized that consists of parallel inputs to the pontine nuclei from the lateral geniculate…

Visualizing Transmedia Networks: Links, Paths and Peripheries

ERIC Educational Resources Information Center

Ruppel, Marc Nathaniel

2012-01-01

'Visualizing Transmedia Networks: Links, Paths and Peripheries' examines the increasingly complex rhetorical intersections between narrative and media ("old" and "new") in the creation of transmedia fictions, loosely defined as multisensory and multimodal stories told extensively across a diverse media set. In order…

The Glycerate and Phosphorylated Pathways of Serine Synthesis in Plants: The Branches of Plant Glycolysis Linking Carbon and Nitrogen Metabolism.

PubMed

Igamberdiev, Abir U; Kleczkowski, Leszek A

2018-01-01

Serine metabolism in plants has been studied mostly in relation to photorespiration where serine is formed from two molecules of glycine. However, two other pathways of serine formation operate in plants and represent the branches of glycolysis diverging at the level of 3-phosphoglyceric acid. One branch (the glycerate - serine pathway) is initiated in the cytosol and involves glycerate formation from 3-phosphoglycerate, while the other (the phosphorylated serine pathway) operates in plastids and forms phosphohydroxypyruvate as an intermediate. Serine formed in these pathways becomes a precursor of glycine, formate and glycolate accumulating in stress conditions. The pathways can be linked to GABA shunt via transamination reactions and via participation of the same reductase for both glyoxylate and succinic semialdehyde. In this review paper we present a hypothesis of the regulation of redox balance in stressed plant cells via participation of the reactions associated with glycerate and phosphorylated serine pathways. We consider these pathways as important processes linking carbon and nitrogen metabolism and maintaining cellular redox and energy levels in stress conditions.

Spontaneous in-flight accommodation of hand orientation to unseen grasp targets: A case of action blindsight.

PubMed

Prentiss, Emily K; Schneider, Colleen L; Williams, Zoë R; Sahin, Bogachan; Mahon, Bradford Z

2018-03-15

The division of labour between the dorsal and ventral visual pathways is well established. The ventral stream supports object identification, while the dorsal stream supports online processing of visual information in the service of visually guided actions. Here, we report a case of an individual with a right inferior quadrantanopia who exhibited accurate spontaneous rotation of his wrist when grasping a target object in his blind visual field. His accurate wrist orientation was observed despite the fact that he exhibited no sensitivity to the orientation of the handle in a perceptual matching task. These findings indicate that non-geniculostriate visual pathways process basic volumetric information relevant to grasping, and reinforce the observation that phenomenal awareness is not necessary for an object's volumetric properties to influence visuomotor performance.

ChemProt-2.0: visual navigation in a disease chemical biology database

PubMed Central

Kim Kjærulff, Sonny; Wich, Louis; Kringelum, Jens; Jacobsen, Ulrik P.; Kouskoumvekaki, Irene; Audouze, Karine; Lund, Ole; Brunak, Søren; Oprea, Tudor I.; Taboureau, Olivier

2013-01-01

ChemProt-2.0 (http://www.cbs.dtu.dk/services/ChemProt-2.0) is a public available compilation of multiple chemical–protein annotation resources integrated with diseases and clinical outcomes information. The database has been updated to >1.15 million compounds with 5.32 millions bioactivity measurements for 15 290 proteins. Each protein is linked to quality-scored human protein–protein interactions data based on more than half a million interactions, for studying diseases and biological outcomes (diseases, pathways and GO terms) through protein complexes. In ChemProt-2.0, therapeutic effects as well as adverse drug reactions have been integrated allowing for suggesting proteins associated to clinical outcomes. New chemical structure fingerprints were computed based on the similarity ensemble approach. Protein sequence similarity search was also integrated to evaluate the promiscuity of proteins, which can help in the prediction of off-target effects. Finally, the database was integrated into a visual interface that enables navigation of the pharmacological space for small molecules. Filtering options were included in order to facilitate and to guide dynamic search of specific queries. PMID:23185041

Building a Linked Learning Pathway: A Guide for Transforming High Schools for College and Career Success

ERIC Educational Resources Information Center

Atterbury, Rob

2014-01-01

This guide provides an overview of a more robust online guide and toolkit available through ConnectEd Studios. It supplies a glimpse of the sequence of steps involved in creating a new Linked Learning pathway. This publication can help coaches, district leadership, and pathway teams gain an understanding of the overall process of designing and…

Vision and visualization.

PubMed

Wade, Nicholas J

2008-01-01

The art of visual communication is not restricted to the fine arts. Scientists also apply art in communicating their ideas graphically. Diagrams of anatomical structures, like the eye and visual pathways, and figures displaying specific visual phenomena have assisted in the communication of visual ideas for centuries. It is often the case that the development of a discipline can be traced through graphical representations and this is explored here in the context of concepts of visual science. As with any science, vision can be subdivided in a variety of ways. The classification adopted is in terms of optics, anatomy, and visual phenomena; each of these can in turn be further subdivided. Optics can be considered in terms of the nature of light and its transmission through the eye. Understanding of the gross anatomy of the eye and visual pathways was initially dependent upon the skills of the anatomist whereas microanatomy relied to a large extent on the instruments that could resolve cellular detail, allied to the observational skills of the microscopist. Visual phenomena could often be displayed on the printed page, although novel instruments expanded the scope of seeing, particularly in the nineteenth century.

Mapping the Primate Visual System with [2-14C]Deoxyglucose

NASA Astrophysics Data System (ADS)

Macko, Kathleen A.; Jarvis, Charlene D.; Kennedy, Charles; Miyaoka, Mikoto; Shinohara, Mami; Sokoloff, Louis; Mishkin, Mortimer

1982-10-01

The [2-14C]deoxyglucose method was used to identify the cerebral areas related to vision in the rhesus monkey (Macaca mulatta). This was achieved by comparing glucose utilization in a visually stimulated with that in a visually deafferented hemisphere. The cortical areas related to vision included the entire expanse of striate, prestriate, and inferior temporal cortex as far forward as the temporal pole, the posterior part of the inferior parietal lobule, and the prearcuate and inferior prefrontal cortex. Subcortically, in addition to the dorsal lateral geniculate nucleus and superficial layers of the superior colliculus, the structures related to vision included large parts of the pulvinar, caudate, putamen, claustrum, and amygdala. These results, which are consonant with a model of visual function that postulates an occipito-temporo-prefrontal pathway for object vision and an occipito-parieto-prefrontal pathway for spatial vision, reveal the full extent of those pathways and identify their points of contact with limbic, striatal, and diencephalic structures.

Asymmetric temporal integration of layer 4 and layer 2/3 inputs in visual cortex.

PubMed

Hang, Giao B; Dan, Yang

2011-01-01

Neocortical neurons in vivo receive concurrent synaptic inputs from multiple sources, including feedforward, horizontal, and feedback pathways. Layer 2/3 of the visual cortex receives feedforward input from layer 4 and horizontal input from layer 2/3. Firing of the pyramidal neurons, which carries the output to higher cortical areas, depends critically on the interaction of these pathways. Here we examined synaptic integration of inputs from layer 4 and layer 2/3 in rat visual cortical slices. We found that the integration is sublinear and temporally asymmetric, with larger responses if layer 2/3 input preceded layer 4 input. The sublinearity depended on inhibition, and the asymmetry was largely attributable to the difference between the two inhibitory inputs. Interestingly, the asymmetric integration was specific to pyramidal neurons, and it strongly affected their spiking output. Thus via cortical inhibition, the temporal order of activation of layer 2/3 and layer 4 pathways can exert powerful control of cortical output during visual processing.

Improving Dorsal Stream Function in Dyslexics by Training Figure/Ground Motion Discrimination Improves Attention, Reading Fluency, and Working Memory

PubMed Central

Lawton, Teri

2016-01-01

There is an ongoing debate about whether the cause of dyslexia is based on linguistic, auditory, or visual timing deficits. To investigate this issue three interventions were compared in 58 dyslexics in second grade (7 years on average), two targeting the temporal dynamics (timing) of either the auditory or visual pathways with a third reading intervention (control group) targeting linguistic word building. Visual pathway training in dyslexics to improve direction-discrimination of moving test patterns relative to a stationary background (figure/ground discrimination) significantly improved attention, reading fluency, both speed and comprehension, phonological processing, and both auditory and visual working memory relative to controls, whereas auditory training to improve phonological processing did not improve these academic skills significantly more than found for controls. This study supports the hypothesis that faulty timing in synchronizing the activity of magnocellular with parvocellular visual pathways is a fundamental cause of dyslexia, and argues against the assumption that reading deficiencies in dyslexia are caused by phonological deficits. This study demonstrates that visual movement direction-discrimination can be used to not only detect dyslexia early, but also for its successful treatment, so that reading problems do not prevent children from readily learning. PMID:27551263

Atypical form of Alzheimer's disease with prominent posterior cortical atrophy: a review of lesion distribution and circuit disconnection in cortical visual pathways

NASA Technical Reports Server (NTRS)

Hof, P. R.; Vogt, B. A.; Bouras, C.; Morrison, J. H.; Bloom, F. E. (Principal Investigator)

1997-01-01

In recent years, the existence of visual variants of Alzheimer's disease characterized by atypical clinical presentation at onset has been increasingly recognized. In many of these cases post-mortem neuropathological assessment revealed that correlations could be established between clinical symptoms and the distribution of neurodegenerative lesions. We have analyzed a series of Alzheimer's disease patients presenting with prominent visual symptomatology as a cardinal sign of the disease. In these cases, a shift in the distribution of pathological lesions was observed such that the primary visual areas and certain visual association areas within the occipito-parieto-temporal junction and posterior cingulate cortex had very high densities of lesions, whereas the prefrontal cortex had fewer lesions than usually observed in Alzheimer's disease. Previous quantitative analyses have demonstrated that in Alzheimer's disease, primary sensory and motor cortical areas are less damaged than the multimodal association areas of the frontal and temporal lobes, as indicated by the laminar and regional distribution patterns of neurofibrillary tangles and senile plaques. The distribution of pathological lesions in the cerebral cortex of Alzheimer's disease cases with visual symptomatology revealed that specific visual association pathways were disrupted, whereas these particular connections are likely to be affected to a less severe degree in the more common form of Alzheimer's disease. These data suggest that in some cases with visual variants of Alzheimer's disease, the neurological symptomatology may be related to the loss of certain components of the cortical visual pathways, as reflected by the particular distribution of the neuropathological markers of the disease.

Colour-induced relationship between affect and reaching kinematics during a goal-directed aiming task.

PubMed

Williams, Camille K; Grierson, Lawrence E M; Carnahan, Heather

2011-08-01

A link between affect and action has been supported by the discovery that threat information is prioritized through an action-centred pathway--the dorsal visual stream. Magnocellular afferents, which originate from the retina and project to dorsal stream structures, are suppressed by exposure to diffuse red light, which diminishes humans' perception of threat-based images. In order to explore the role of colour in the relationship between affect and action, participants donned different pairs of coloured glasses (red, yellow, green, blue and clear) and completed Positive and Negative Affect Scale questionnaires as well as a series of target-directed aiming movements. Analyses of affect scores revealed a significant main effect for affect valence and a significant interaction between colour and valence: perceived positive affect was significantly smaller for the red condition. Kinematic analyses of variable error in the primary movement direction and Pearson correlation analyses between the displacements travelled prior to and following peak velocity indicated reduced accuracy and application of online control processes while wearing red glasses. Variable error of aiming was also positively and significantly correlated with negative affect scores under the red condition. These results suggest that only red light modulates the affect-action link by suppressing magnocellular activity, which disrupts visual processing for movement control. Furthermore, previous research examining the effect of the colour red on psychomotor tasks and perceptual acceleration of threat-based imagery suggest that stimulus-driven motor performance tasks requiring online control may be particularly susceptible to this effect.

Students using visual thinking to learn science in a Web-based environment

NASA Astrophysics Data System (ADS)

Plough, Jean Margaret

United States students' science test scores are low, especially in problem solving, and traditional science instruction could be improved. Consequently, visual thinking, constructing science structures, and problem solving in a web-based environment may be valuable strategies for improving science learning. This ethnographic study examined the science learning of fifteen fourth grade students in an after school computer club involving diverse students at an inner city school. The investigation was done from the perspective of the students, and it described the processes of visual thinking, web page construction, and problem solving in a web-based environment. The study utilized informal group interviews, field notes, Visual Learning Logs, and student web pages, and incorporated a Standards-Based Rubric which evaluated students' performance on eight science and technology standards. The Visual Learning Logs were drawings done on the computer to represent science concepts related to the Food Chain. Students used the internet to search for information on a plant or animal of their choice. Next, students used this internet information, with the information from their Visual Learning Logs, to make web pages on their plant or animal. Later, students linked their web pages to form Science Structures. Finally, students linked their Science Structures with the structures of other students, and used these linked structures as models for solving problems. Further, during informal group interviews, students answered questions about visual thinking, problem solving, and science concepts. The results of this study showed clearly that (1) making visual representations helped students understand science knowledge, (2) making links between web pages helped students construct Science Knowledge Structures, and (3) students themselves said that visual thinking helped them learn science. In addition, this study found that when using Visual Learning Logs, the main overall ideas of the science concepts were usually represented accurately. Further, looking for information on the internet may cause new problems in learning. Likewise, being absent, starting late, and/or dropping out all may negatively influence students' proficiency on the standards. Finally, the way Science Structures are constructed and linked may provide insights into the way individual students think and process information.

Integration of bio-inspired, control-based visual and olfactory data for the detection of an elusive target

NASA Astrophysics Data System (ADS)

Duong, Tuan A.; Duong, Nghi; Le, Duong

2017-01-01

In this paper, we present an integration technique using a bio-inspired, control-based visual and olfactory receptor system to search for elusive targets in practical environments where the targets cannot be seen obviously by either sensory data. Bio-inspired Visual System is based on a modeling of extended visual pathway which consists of saccadic eye movements and visual pathway (vertebrate retina, lateral geniculate nucleus and visual cortex) to enable powerful target detections of noisy, partial, incomplete visual data. Olfactory receptor algorithm, namely spatial invariant independent component analysis, that was developed based on data of old factory receptor-electronic nose (enose) of Caltech, is adopted to enable the odorant target detection in an unknown environment. The integration of two systems is a vital approach and sets up a cornerstone for effective and low-cost of miniaturized UAVs or fly robots for future DOD and NASA missions, as well as for security systems in Internet of Things environments.

Reactome diagram viewer: data structures and strategies to boost performance.

PubMed

Fabregat, Antonio; Sidiropoulos, Konstantinos; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-04-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. For web-based pathway visualization, Reactome uses a custom pathway diagram viewer that has been evolved over the past years. Here, we present comprehensive enhancements in usability and performance based on extensive usability testing sessions and technology developments, aiming to optimize the viewer towards the needs of the community. The pathway diagram viewer version 3 achieves consistently better performance, loading and rendering of 97% of the diagrams in Reactome in less than 1 s. Combining the multi-layer html5 canvas strategy with a space partitioning data structure minimizes CPU workload, enabling the introduction of new features that further enhance user experience. Through the use of highly optimized data structures and algorithms, Reactome has boosted the performance and usability of the new pathway diagram viewer, providing a robust, scalable and easy-to-integrate solution to pathway visualization. As graph-based visualization of complex data is a frequent challenge in bioinformatics, many of the individual strategies presented here are applicable to a wide range of web-based bioinformatics resources. Reactome is available online at: https://reactome.org. The diagram viewer is part of the Reactome pathway browser (https://reactome.org/PathwayBrowser/) and also available as a stand-alone widget at: https://reactome.org/dev/diagram/. The source code is freely available at: https://github.com/reactome-pwp/diagram. fabregat@ebi.ac.uk or hhe@ebi.ac.uk. Supplementary data are available at Bioinformatics online.

Visual disability rates in a ten-year cohort of patients with anterior visual pathway meningiomas.

PubMed

Bor-Shavit, Elite; Hammel, Naama; Nahum, Yoav; Rappaport, Zvi Harry; Stiebel-Kalish, Hadas

2015-01-01

To examine the visual outcome of anterior visual pathway meningioma (AVPM) patients followed for at least one year. Data were collected on demographics, clinical course and management. Visual disability was classified at the first and last examination as follows: I--no visual disability; II--mild visual defect in one eye; III--mild visual defect in both eyes; IV--loss of driver's license; V--legally blind. Eight-one AVPM patients had their tumor originate in the clinoid process in 23 (28%), sphenoid-wing area in 18 (22%), cavernous sinus in 15 (19%), tuberculum sellae in 8 (10%), and mixed in 17 (21%). On last examination, 46 patients (57%) had good visual acuity in one or both eyes (Class I or II) and 17 (21%) were mildly affected in both eyes. The rate of Class IV disability was 16%, and Class V disability was 6%. Attention needs to be addressed to the considerable proportion of patients with AVPM (22% in this study) who may lose their driver's license or become legally blind. Occupational therapists should play an important role in the multidisciplinary management of those patients to help them adapt to their new physical and social situation. Anterior visual pathway meningiomas (AVPMs) are commonly not life-threatening but they can lead to profound visual disability, especially when the tumor originates in the tuberculum sellae and cavernous sinus. Particular attention should be paid to visual acuity and visual field deficits, as these can profoundly affect the patient's quality of life including ability to drive and activities of daily living. The interdisciplinary management of patients with AVPM should include the neurosurgeon, neuro-ophthalmologist and occupational therapist. Also, early intervention by the occupational therapist can help patients adapt to their current physical and social situation and return to everyday tasks more rapidly.

Selective neural pathway targeting reveals key roles of thalamostriatal projection in the control of visual discrimination.

PubMed

Kato, Shigeki; Kuramochi, Masahito; Kobayashi, Kenta; Fukabori, Ryoji; Okada, Kana; Uchigashima, Motokazu; Watanabe, Masahiko; Tsutsui, Yuji; Kobayashi, Kazuto

2011-11-23

The dorsal striatum receives converging excitatory inputs from diverse brain regions, including the cerebral cortex and the intralaminar/midline thalamic nuclei, and mediates learning processes contributing to instrumental motor actions. However, the roles of each striatal input pathway in these learning processes remain uncertain. We developed a novel strategy to target specific neural pathways and applied this strategy for studying behavioral roles of the pathway originating from the parafascicular nucleus (PF) and projecting to the dorsolateral striatum. A highly efficient retrograde gene transfer vector encoding the recombinant immunotoxin (IT) receptor was injected into the dorsolateral striatum in mice to express the receptor in neurons innervating the striatum. IT treatment into the PF of the vector-injected animals caused a selective elimination of neurons of the PF-derived thalamostriatal pathway. The elimination of this pathway impaired the response selection accuracy and delayed the motor response in the acquisition of a visual cue-dependent discrimination task. When the pathway elimination was induced after learning acquisition, it disturbed the response accuracy in the task performance with no apparent change in the response time. The elimination did not influence spontaneous locomotion, methamphetamine-induced hyperactivity, and motor skill learning that demand the function of the dorsal striatum. These results demonstrate that thalamostriatal projection derived from the PF plays essential roles in the acquisition and execution of discrimination learning in response to sensory stimulus. The temporal difference in the pathway requirement for visual discrimination suggests a stage-specific role of thalamostriatal pathway in the modulation of response time of learned motor actions.

EdgeMaps: visualizing explicit and implicit relations

NASA Astrophysics Data System (ADS)

Dörk, Marian; Carpendale, Sheelagh; Williamson, Carey

2011-01-01

In this work, we introduce EdgeMaps as a new method for integrating the visualization of explicit and implicit data relations. Explicit relations are specific connections between entities already present in a given dataset, while implicit relations are derived from multidimensional data based on shared properties and similarity measures. Many datasets include both types of relations, which are often difficult to represent together in information visualizations. Node-link diagrams typically focus on explicit data connections, while not incorporating implicit similarities between entities. Multi-dimensional scaling considers similarities between items, however, explicit links between nodes are not displayed. In contrast, EdgeMaps visualize both implicit and explicit relations by combining and complementing spatialization and graph drawing techniques. As a case study for this approach we chose a dataset of philosophers, their interests, influences, and birthdates. By introducing the limitation of activating only one node at a time, interesting visual patterns emerge that resemble the aesthetics of fireworks and waves. We argue that the interactive exploration of these patterns may allow the viewer to grasp the structure of a graph better than complex node-link visualizations.

Visualizing weighted networks: a performance comparison of adjacency matrices versus node-link diagrams

NASA Astrophysics Data System (ADS)

McIntire, John P.; Osesina, O. Isaac; Bartley, Cecilia; Tudoreanu, M. Eduard; Havig, Paul R.; Geiselman, Eric E.

2012-06-01

Ensuring the proper and effective ways to visualize network data is important for many areas of academia, applied sciences, the military, and the public. Fields such as social network analysis, genetics, biochemistry, intelligence, cybersecurity, neural network modeling, transit systems, communications, etc. often deal with large, complex network datasets that can be difficult to interact with, study, and use. There have been surprisingly few human factors performance studies on the relative effectiveness of different graph drawings or network diagram techniques to convey information to a viewer. This is particularly true for weighted networks which include the strength of connections between nodes, not just information about which nodes are linked to other nodes. We describe a human factors study in which participants performed four separate network analysis tasks (finding a direct link between given nodes, finding an interconnected node between given nodes, estimating link strengths, and estimating the most densely interconnected nodes) on two different network visualizations: an adjacency matrix with a heat-map versus a node-link diagram. The results should help shed light on effective methods of visualizing network data for some representative analysis tasks, with the ultimate goal of improving usability and performance for viewers of network data displays.

Posterior Inferotemporal Cortex Cells Use Multiple Input Pathways for Shape Encoding.

PubMed

Ponce, Carlos R; Lomber, Stephen G; Livingstone, Margaret S

2017-05-10

In the macaque monkey brain, posterior inferior temporal (PIT) cortex cells contribute to visual object recognition. They receive concurrent inputs from visual areas V4, V3, and V2. We asked how these different anatomical pathways shape PIT response properties by deactivating them while monitoring PIT activity in two male macaques. We found that cooling of V4 or V2|3 did not lead to consistent changes in population excitatory drive; however, population pattern analyses showed that V4-based pathways were more important than V2|3-based pathways. We did not find any image features that predicted decoding accuracy differences between both interventions. Using the HMAX hierarchical model of visual recognition, we found that different groups of simulated "PIT" units with different input histories (lacking "V2|3" or "V4" input) allowed for comparable levels of object-decoding performance and that removing a large fraction of "PIT" activity resulted in similar drops in performance as in the cooling experiments. We conclude that distinct input pathways to PIT relay similar types of shape information, with V1-dependent V4 cells providing more quantitatively useful information for overall encoding than cells in V2 projecting directly to PIT. SIGNIFICANCE STATEMENT Convolutional neural networks are the best models of the visual system, but most emphasize input transformations across a serial hierarchy akin to the primary "ventral stream" (V1 → V2 → V4 → IT). However, the ventral stream also comprises parallel "bypass" pathways: V1 also connects to V4, and V2 to IT. To explore the advantages of mixing long and short pathways in the macaque brain, we used cortical cooling to silence inputs to posterior IT and compared the findings with an HMAX model with parallel pathways. Copyright © 2017 the authors 0270-6474/17/375019-16$15.00/0.

Posterior Inferotemporal Cortex Cells Use Multiple Input Pathways for Shape Encoding

PubMed Central

2017-01-01

In the macaque monkey brain, posterior inferior temporal (PIT) cortex cells contribute to visual object recognition. They receive concurrent inputs from visual areas V4, V3, and V2. We asked how these different anatomical pathways shape PIT response properties by deactivating them while monitoring PIT activity in two male macaques. We found that cooling of V4 or V2|3 did not lead to consistent changes in population excitatory drive; however, population pattern analyses showed that V4-based pathways were more important than V2|3-based pathways. We did not find any image features that predicted decoding accuracy differences between both interventions. Using the HMAX hierarchical model of visual recognition, we found that different groups of simulated “PIT” units with different input histories (lacking “V2|3” or “V4” input) allowed for comparable levels of object-decoding performance and that removing a large fraction of “PIT” activity resulted in similar drops in performance as in the cooling experiments. We conclude that distinct input pathways to PIT relay similar types of shape information, with V1-dependent V4 cells providing more quantitatively useful information for overall encoding than cells in V2 projecting directly to PIT. SIGNIFICANCE STATEMENT Convolutional neural networks are the best models of the visual system, but most emphasize input transformations across a serial hierarchy akin to the primary “ventral stream” (V1 → V2 → V4 → IT). However, the ventral stream also comprises parallel “bypass” pathways: V1 also connects to V4, and V2 to IT. To explore the advantages of mixing long and short pathways in the macaque brain, we used cortical cooling to silence inputs to posterior IT and compared the findings with an HMAX model with parallel pathways. PMID:28416597

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.

PubMed

Wrzodek, Clemens; Dräger, Andreas; Zell, Andreas

2011-08-15

The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. KEGGtranslator is freely available as a Java(™) Web Start application and for download at http://www.cogsys.cs.uni-tuebingen.de/software/KEGGtranslator/. KGML files can be downloaded from within the application. clemens.wrzodek@uni-tuebingen.de Supplementary data are available at Bioinformatics online.

Developmental Pathways from Child Maltreatment to Adolescent Substance Use: The Roles of Posttraumatic Stress Symptoms and Mother-Child Relationships

PubMed Central

Yoon, Susan; Kobulsky, Julia M.; Yoon, Dalhee; Kim, Wonhee

2018-01-01

While many studies have identified a significant relation between child maltreatment and adolescent substance use, the developmental pathways linking this relation remain sparsely explored. The current study examines posttraumatic stress (PTS) symptoms, mother-child relationships, and internalizing and externalizing problems as potential longitudinal pathways through which child maltreatment influences adolescent substance use. Structural equation modeling was conducted on 883 adolescents drawn from the Longitudinal Studies of Child Abuse and Neglect (LONGSCAN). The pathways of PTS symptoms linked physical and sexual abuse to substance use, and the pathways of mother-child relationships linked emotional abuse and neglect to substance use. None of the four types of maltreatment affected substance use via internalizing or externalizing problems. The findings suggest that intervention efforts aimed at addressing posttraumatic stress symptoms and improving mother-child relationship quality may be beneficial in reducing substance use among adolescents with child maltreatment histories. PMID:29503490

Processing Of Visual Information In Primate Brains

NASA Technical Reports Server (NTRS)

Anderson, Charles H.; Van Essen, David C.

1991-01-01

Report reviews and analyzes information-processing strategies and pathways in primate retina and visual cortex. Of interest both in biological fields and in such related computational fields as artificial neural networks. Focuses on data from macaque, which has superb visual system similar to that of humans. Authors stress concept of "good engineering" in understanding visual system.

M-Stream Deficits and Reading-Related Visual Processes in Developmental Dyslexia

ERIC Educational Resources Information Center

Boden, Catherine; Giaschi, Deborah

2007-01-01

Some visual processing deficits in developmental dyslexia have been attributed to abnormalities in the subcortical M stream and/or the cortical dorsal stream of the visual pathways. The nature of the relationship between these visual deficits and reading is unknown. The purpose of the present article was to characterize reading-related perceptual…

The Dual Role of Media Internalization in Adolescent Sexual Behavior.

PubMed

Rousseau, Ann; Beyens, Ine; Eggermont, Steven; Vandenbosch, Laura

2017-08-01

Sexualizing media content is prevalent in various media types. Sexualizing media messages and portrayals emphasize unattainable body and appearance ideals as the primary components of sexual desirability. The internalization of these ideals is positively related to self-objectification and sexual body consciousness. In turn, self-objectification and sexual body consciousness affect adolescents' sexual behavior, albeit in opposing directions. While objectifying self-perceptions are linked to higher levels of sexual behavior, body consciousness during physical intimacy is linked to lower levels of sexual behavior. Based on this knowledge, the present three-wave panel study of 824 Belgian, predominant heterosexual adolescents (M age  = 15.33; SD = 1.45) proposes a dual-pathway model that investigates two different pathways through which the internalization of media ideals may impact adolescents' sexual behavior. An inhibitory pathway links media internalization to lower levels of sexual behavior through sexual body consciousness, and a supportive pathway links media internalization to higher levels of sexual behavior through self-objectification. Structural equation analyses supported the proposed dual-pathway, showing that the impact of media internalization on adolescents' sexual behavior proceeds through an inhibitory pathway and a supportive pathway. Regarding the supportive pathway, media internalization (W1) positively predicted sexual behavior (W3), through valuing appearance over competence (W2). Regarding the inhibitory pathway, media internalization (W1) positively predicted body surveillance, which, in turn, positively predicted sexual body consciousness (all W2). Sexual body consciousness (W2) is negatively related to sexual behavior (W3). From a sexual developmental perspective, these findings emphasize the importance of guiding adolescents in interpreting and processing sexualizing media messages.

Auditory, visual, and bimodal data link displays and how they support pilot performance.

PubMed

Steelman, Kelly S; Talleur, Donald; Carbonari, Ronald; Yamani, Yusuke; Nunes, Ashley; McCarley, Jason S

2013-06-01

The design of data link messaging systems to ensure optimal pilot performance requires empirical guidance. The current study examined the effects of display format (auditory, visual, or bimodal) and visual display position (adjacent to instrument panel or mounted on console) on pilot performance. Subjects performed five 20-min simulated single-pilot flights. During each flight, subjects received messages from a simulated air traffic controller. Messages were delivered visually, auditorily, or bimodally. Subjects were asked to read back each message aloud and then perform the instructed maneuver. Visual and bimodal displays engendered lower subjective workload and better altitude tracking than auditory displays. Readback times were shorter with the two unimodal visual formats than with any of the other three formats. Advantages for the unimodal visual format ranged in size from 2.8 s to 3.8 s relative to the bimodal upper left and auditory formats, respectively. Auditory displays allowed slightly more head-up time (3 to 3.5 seconds per minute) than either visual or bimodal displays. Position of the visual display had only modest effects on any measure. Combined with the results from previous studies by Helleberg and Wickens and Lancaster and Casali the current data favor visual and bimodal displays over auditory displays; unimodal auditory displays were favored by only one measure, head-up time, and only very modestly. Data evinced no statistically significant effects of visual display position on performance, suggesting that, contrary to expectations, the placement of a visual data link display may be of relatively little consequence to performance.

Visualizing Rank Time Series of Wikipedia Top-Viewed Pages.

PubMed

Xia, Jing; Hou, Yumeng; Chen, Yingjie Victor; Qian, Zhenyu Cheryl; Ebert, David S; Chen, Wei

2017-01-01

Visual clutter is a common challenge when visualizing large rank time series data. WikiTopReader, a reader of Wikipedia page rank, lets users explore connections among top-viewed pages by connecting page-rank behaviors with page-link relations. Such a combination enhances the unweighted Wikipedia page-link network and focuses attention on the page of interest. A set of user evaluations shows that the system effectively represents evolving ranking patterns and page-wise correlation.

The Use of Signal-Transduction and Metabolic Pathways to Predict Human Disease Targets from Electric and Magnetic Fields Using in vitro Data in Human Cell Lines

PubMed Central

Parham, Fred; Portier, Christopher J.; Chang, Xiaoqing; Mevissen, Meike

2016-01-01

Using in vitro data in human cell lines, several research groups have investigated changes in gene expression in cellular systems following exposure to extremely low frequency (ELF) and radiofrequency (RF) electromagnetic fields (EMF). For ELF EMF, we obtained five studies with complete microarray data and three studies with only lists of significantly altered genes. Likewise, for RF EMF, we obtained 13 complete microarray datasets and 5 limited datasets. Plausible linkages between exposure to ELF and RF EMF and human diseases were identified using a three-step process: (a) linking genes associated with classes of human diseases to molecular pathways, (b) linking pathways to ELF and RF EMF microarray data, and (c) identifying associations between human disease and EMF exposures where the pathways are significantly similar. A total of 60 pathways were associated with human diseases, mostly focused on basic cellular functions like JAK–STAT signaling or metabolic functions like xenobiotic metabolism by cytochrome P450 enzymes. ELF EMF datasets were sporadically linked to human diseases, but no clear pattern emerged. Individual datasets showed some linkage to cancer, chemical dependency, metabolic disorders, and neurological disorders. RF EMF datasets were not strongly linked to any disorders but strongly linked to changes in several pathways. Based on these analyses, the most promising area for further research would be to focus on EMF and neurological function and disorders. PMID:27656641

How Does the Hippocampal Formation Mediate Memory for Stimuli Processed by the Magnocellular and Parvocellular Visual Pathways? Evidence from the Comparison of Schizophrenia and Amnestic Mild Cognitive Impairment (aMCI)

ERIC Educational Resources Information Center

Keri, Szabolcs; Szamosi, Andras; Benedek, Gyorgy; Kelemen, Oguz

2012-01-01

Paired associates learning is impaired in both schizophrenia and amnestic mild cognitive impairment (aMCI), which may reflect hippocampal pathology. In addition, schizophrenia is characterized by the dysfunction of the retino-geniculo-striatal magnocellular (M) visual pathway. The purpose of this study was to investigate the interaction between…

BMDExpress Data Viewer: A Visualization Tool to Analyze ...

EPA Pesticide Factsheets

Regulatory agencies increasingly apply benchmark dose (BMD) modeling to determine points of departure in human risk assessments. BMDExpress applies BMD modeling to transcriptomics datasets and groups genes to biological processes and pathways for rapid assessment of doses at which biological perturbations occur. However, graphing and analytical capabilities within BMDExpress are limited, and the analysis of output files is challenging. We developed a web-based application, BMDExpress Data Viewer, for visualization and graphical analyses of BMDExpress output files. The software application consists of two main components: ‘Summary Visualization Tools’ and ‘Dataset Exploratory Tools’. We demonstrate through two case studies that the ‘Summary Visualization Tools’ can be used to examine and assess the distributions of probe and pathway BMD outputs, as well as derive a potential regulatory BMD through the modes or means of the distributions. The ‘Functional Enrichment Analysis’ tool presents biological processes in a two-dimensional bubble chart view. By applying filters of pathway enrichment p-value and minimum number of significant genes, we showed that the Functional Enrichment Analysis tool can be applied to select pathways that are potentially sensitive to chemical perturbations. The ‘Multiple Dataset Comparison’ tool enables comparison of BMDs across multiple experiments (e.g., across time points, tissues, or organisms, etc.). The ‘BMDL-BM

Vasopressin Proves Es-sense-tial: Vasopressin and the Modulation of Sensory Processing in Mammals

PubMed Central

Bester-Meredith, Janet K.; Fancher, Alexandria P.; Mammarella, Grace E.

2015-01-01

As mammals develop, they encounter increasing social complexity in the surrounding world. In order to survive, mammals must show appropriate behaviors toward their mates, offspring, and same-sex conspecifics. Although the behavioral effects of the neuropeptide arginine vasopressin (AVP) have been studied in a variety of social contexts, the effects of this neuropeptide on multimodal sensory processing have received less attention. AVP is widely distributed through sensory regions of the brain and has been demonstrated to modulate olfactory, auditory, gustatory, and visual processing. Here, we review the evidence linking AVP to the processing of social stimuli in sensory regions of the brain and explore how sensory processing can shape behavioral responses to these stimuli. In addition, we address the interplay between hormonal and neural AVP in regulating sensory processing of social cues. Because AVP pathways show plasticity during development, early life experiences may shape life-long processing of sensory information. Furthermore, disorders of social behavior such as autism and schizophrenia that have been linked with AVP also have been linked with dysfunctions in sensory processing. Together, these studies suggest that AVP’s diversity of effects on social behavior across a variety of mammalian species may result from the effects of this neuropeptide on sensory processing. PMID:25705203

Neural substrates underlying fear-evoked freezing: the periaqueductal grey–cerebellar link

PubMed Central

Koutsikou, Stella; Crook, Jonathan J; Earl, Emma V; Leith, J Lianne; Watson, Thomas C; Lumb, Bridget M; Apps, Richard

2014-01-01

The central neural pathways involved in fear-evoked behaviour are highly conserved across mammalian species, and there is a consensus that understanding them is a fundamental step towards developing effective treatments for emotional disorders in man. The ventrolateral periaqueductal grey (vlPAG) has a well-established role in fear-evoked freezing behaviour. The neural pathways underlying autonomic and sensory consequences of vlPAG activation in fearful situations are well understood, but much less is known about the pathways that link vlPAG activity to distinct fear-evoked motor patterns essential for survival. In adult rats, we have identified a pathway linking the vlPAG to cerebellar cortex, which terminates as climbing fibres in lateral vermal lobule VIII (pyramis). Lesion of pyramis input–output pathways disrupted innate and fear-conditioned freezing behaviour. The disruption in freezing behaviour was strongly correlated to the reduction in the vlPAG-induced facilitation of α-motoneurone excitability observed after lesions of the pyramis. The increased excitability of α-motoneurones during vlPAG activation may therefore drive the increase in muscle tone that underlies expression of freezing behaviour. By identifying the cerebellar pyramis as a critical component of the neural network subserving emotionally related freezing behaviour, the present study identifies novel neural pathways that link the PAG to fear-evoked motor responses. PMID:24639484

FNV: light-weight flash-based network and pathway viewer.

PubMed

Dannenfelser, Ruth; Lachmann, Alexander; Szenk, Mariola; Ma'ayan, Avi

2011-04-15

Network diagrams are commonly used to visualize biochemical pathways by displaying the relationships between genes, proteins, mRNAs, microRNAs, metabolites, regulatory DNA elements, diseases, viruses and drugs. While there are several currently available web-based pathway viewers, there is still room for improvement. To this end, we have developed a flash-based network viewer (FNV) for the visualization of small to moderately sized biological networks and pathways. Written in Adobe ActionScript 3.0, the viewer accepts simple Extensible Markup Language (XML) formatted input files to display pathways in vector graphics on any web-page providing flexible layout options, interactivity with the user through tool tips, hyperlinks and the ability to rearrange nodes on the screen. FNV was utilized as a component in several web-based systems, namely Genes2Networks, Lists2Networks, KEA, ChEA and PathwayGenerator. In addition, FVN can be used to embed pathways inside pdf files for the communication of pathways in soft publication materials. FNV is available for use and download along with the supporting documentation and sample networks at http://www.maayanlab.net/FNV. avi.maayan@mssm.edu.

Vision restoration through extrastriate stimulation in patients with visual field defects: a double-blind and randomized experimental study.

PubMed

Jobke, Sandra; Kasten, Erich; Sabel, Bernhard A

2009-01-01

. Vision restoration therapy (VRT) to treat visual field defects used single-point visual stimulation in areas of residual vision up to now. The question arises if the efficiency of restoration can be increased when the entire region of blindness is trained by a visual stimulus aimed at activating extrastriate pathways (extrastriate VRT). . In this crossover study, 18 patients with visual field defects with prior VRT experience were treated with 2 training paradigms. Group 1 (n = 8) first used extrastriate VRT followed by conventional standard VRT. Group 2 (n = 10) trained in reverse order. Visual field size was assessed with computer-based perimetry and subjective vision with the National Eye Institute Visual Function Questionnaire (NEI-VFQ). . In group 1, stimulus detection in high-resolution perimetry (HRP) improved by 5.9% (P < .01) after extrastriate VRT. After the second training period (standard VRT), detection further improved by 1.8% (P = .093). In group 2, detection performance improved after standard VRT by 2.9% (P < .05) and after extrastriate VRT by 2.9% (P < .05). Detection performance increased twice as much after extrastriate VRT (4.2%) than after standard VRT (2.4%; P < .05). All changes in fixation performance were unrelated to detection improvements. NEI-VFQ did not show any significant changes. . Greater improvement after extrastriate VRT is interpreted as an activation of extrastriate pathways by massive "spiral-like" stimulation. These pathways bypass the damaged visual cortex, stimulating extrastriate cortical regions, and are thought to be involved in blindsight.

Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs.

PubMed

Allain, Ariane; Chauvot de Beauchêne, Isaure; Langenfeld, Florent; Guarracino, Yann; Laine, Elodie; Tchertanov, Luba

2014-01-01

Allostery is a universal phenomenon that couples the information induced by a local perturbation (effector) in a protein to spatially distant regulated sites. Such an event can be described in terms of a large scale transmission of information (communication) through a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. To elaborate a rational description of allosteric coupling, we propose an original approach - MOdular NETwork Analysis (MONETA) - based on the analysis of inter-residue dynamical correlations to localize the propagation of both structural and dynamical effects of a perturbation throughout a protein structure. MONETA uses inter-residue cross-correlations and commute times computed from molecular dynamics simulations and a topological description of a protein to build a modular network representation composed of clusters of residues (dynamic segments) linked together by chains of residues (communication pathways). MONETA provides a brand new direct and simple visualization of protein allosteric communication. A GEPHI module implemented in the MONETA package allows the generation of 2D graphs of the communication network. An interactive PyMOL plugin permits drawing of the communication pathways between chosen protein fragments or residues on a 3D representation. MONETA is a powerful tool for on-the-fly display of communication networks in proteins. We applied MONETA for the analysis of communication pathways (i) between the main regulatory fragments of receptors tyrosine kinases (RTKs), KIT and CSF-1R, in the native and mutated states and (ii) in proteins STAT5 (STAT5a and STAT5b) in the phosphorylated and the unphosphorylated forms. The description of the physical support for allosteric coupling by MONETA allowed a comparison of the mechanisms of (a) constitutive activation induced by equivalent mutations in two RTKs and (b) allosteric regulation in the activated and non-activated STAT5 proteins. Our theoretical prediction based on results obtained with MONETA was validated for KIT by in vitro experiments. MONETA is a versatile analytical and visualization tool entirely devoted to the understanding of the functioning/malfunctioning of allosteric regulation in proteins - a crucial basis to guide the discovery of next-generation allosteric drugs.

Enhanced Visual Cortical Activation for Emotional Stimuli is Preserved in Patients with Unilateral Amygdala Resection

PubMed Central

Edmiston, E. Kale; McHugo, Maureen; Dukic, Mildred S.; Smith, Stephen D.; Abou-Khalil, Bassel; Eggers, Erica

2013-01-01

Emotionally arousing pictures induce increased activation of visual pathways relative to emotionally neutral images. A predominant model for the preferential processing and attention to emotional stimuli posits that the amygdala modulates sensory pathways through its projections to visual cortices. However, recent behavioral studies have found intact perceptual facilitation of emotional stimuli in individuals with amygdala damage. To determine the importance of the amygdala to modulations in visual processing, we used functional magnetic resonance imaging to examine visual cortical blood oxygenation level-dependent (BOLD) signal in response to emotionally salient and neutral images in a sample of human patients with unilateral medial temporal lobe resection that included the amygdala. Adults with right (n = 13) or left (n = 5) medial temporal lobe resections were compared with demographically matched healthy control participants (n = 16). In the control participants, both aversive and erotic images produced robust BOLD signal increases in bilateral primary and secondary visual cortices relative to neutral images. Similarly, all patients with amygdala resections showed enhanced visual cortical activations to erotic images both ipsilateral and contralateral to the lesion site. All but one of the amygdala resection patients showed similar enhancements to aversive stimuli and there were no significant group differences in visual cortex BOLD responses in patients compared with controls for either aversive or erotic images. Our results indicate that neither the right nor left amygdala is necessary for the heightened visual cortex BOLD responses observed during emotional stimulus presentation. These data challenge an amygdalo-centric model of emotional modulation and suggest that non-amygdalar processes contribute to the emotional modulation of sensory pathways. PMID:23825407

A Survey of Parents of Children with Cortical or Cerebral Visual Impairment

ERIC Educational Resources Information Center

Jackel, Bernadette; Wilson, Michelle; Hartmann, Elizabeth

2010-01-01

Cortical or cerebral visual impairment (CVI) can result when the visual pathways and visual processing areas of the brain have been damaged. Children with CVI may have difficulty finding an object among other objects, viewing in the distance, orienting themselves in space, going from grass to pavement or other changes in surface, and copying…

Sight and blindness in the same person: Gating in the visual system.

PubMed

Strasburger, Hans; Waldvogel, Bruno

2015-12-01

We present the case of a patient having dissociative identity disorder (DID) who-after 15 years of misdiagnosed cortical blindness--step-by-step regained sight during psychotherapeutic treatment. At first only a few personality states regained vision whereas others remained blind. This could be confirmed by electrophysiological measurement, in which visual evoked potentials (VEPs) were absent in the blind personality states but were normal and stable in the seeing states. A switch between these states could happen within seconds. We assume a top-down modulation of activity in the primary visual pathway as a neural basis of such psychogenic blindness, possibly at the level of the thalamus. VEPs therefore do not allow separating psychogenic blindness from organic disruption of the visual pathway. In summary, psychogenic blindness seems to suppress visual information at an early neural stage. © 2015 The Institute of Psychology, Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

Sharpening of Hierarchical Visual Feature Representations of Blurred Images.

PubMed

Abdelhack, Mohamed; Kamitani, Yukiyasu

2018-01-01

The robustness of the visual system lies in its ability to perceive degraded images. This is achieved through interacting bottom-up, recurrent, and top-down pathways that process the visual input in concordance with stored prior information. The interaction mechanism by which they integrate visual input and prior information is still enigmatic. We present a new approach using deep neural network (DNN) representation to reveal the effects of such integration on degraded visual inputs. We transformed measured human brain activity resulting from viewing blurred images to the hierarchical representation space derived from a feedforward DNN. Transformed representations were found to veer toward the original nonblurred image and away from the blurred stimulus image. This indicated deblurring or sharpening in the neural representation, and possibly in our perception. We anticipate these results will help unravel the interplay mechanism between bottom-up, recurrent, and top-down pathways, leading to more comprehensive models of vision.

Multiple Sensory-Motor Pathways Lead to Coordinated Visual Attention

PubMed Central

Yu, Chen; Smith, Linda B.

2016-01-01

Joint attention has been extensively studied in the developmental literature because of overwhelming evidence that the ability to socially coordinate visual attention to an object is essential to healthy developmental outcomes, including language learning. The goal of the present study is to understand the complex system of sensory-motor behaviors that may underlie the establishment of joint attention between parents and toddlers. In an experimental task, parents and toddlers played together with multiple toys. We objectively measured joint attention – and the sensory-motor behaviors that underlie it – using a dual head-mounted eye-tracking system and frame-by-frame coding of manual actions. By tracking the momentary visual fixations and hand actions of each participant, we precisely determined just how often they fixated on the same object at the same time, the visual behaviors that preceded joint attention, and manual behaviors that preceded and co-occurred with joint attention. We found that multiple sequential sensory-motor patterns lead to joint attention. In addition, there are developmental changes in this multi-pathway system evidenced as variations in strength among multiple routes. We propose that coordinated visual attention between parents and toddlers is primarily a sensory-motor behavior. Skill in achieving coordinated visual attention in social settings – like skills in other sensory-motor domains – emerges from multiple pathways to the same functional end. PMID:27016038

Effects of gestational length, gender, postnatal age, and birth order on visual contrast sensitivity in infants.

PubMed

Dobkins, Karen R; Bosworth, Rain G; McCleery, Joseph P

2009-09-30

To investigate effects of visual experience versus preprogrammed mechanisms on visual development, we used multiple regression analysis to determine the extent to which a variety of variables (that differ in the extent to which they are tied to visual experience) predict luminance and chromatic (red/green) contrast sensitivity (CS), which are mediated by the magnocellular (M) and parvocellular (P) subcortical pathways, respectively. Our variables included gestational length (GL), birth weight (BW), gender, postnatal age (PNA), and birth order (BO). Two-month-olds (n = 60) and 6-month-olds (n = 122) were tested. Results revealed that (1) at 2 months, infants with longer GL have higher luminance CS; (2) at both ages, CS significantly increases over a approximately 21-day range of PNA, but this effect is stronger in 2- than 6-month-olds and stronger for chromatic than luminance CS; (3) at 2 months, boys have higher luminance CS than girls; and (4) at 2 months, firstborn infants have higher CS, while at 6 months, non-firstborn infants have higher CS. The results for PNA/GL are consistent with the possibility that P pathway development is more influenced by variables tied to visual experience (PNA), while M pathway development is more influenced by variables unrelated to visual experience (GL). Other variables, including prenatal environment, are also discussed.

Multiple Sensory-Motor Pathways Lead to Coordinated Visual Attention.

PubMed

Yu, Chen; Smith, Linda B

2017-02-01

Joint attention has been extensively studied in the developmental literature because of overwhelming evidence that the ability to socially coordinate visual attention to an object is essential to healthy developmental outcomes, including language learning. The goal of this study was to understand the complex system of sensory-motor behaviors that may underlie the establishment of joint attention between parents and toddlers. In an experimental task, parents and toddlers played together with multiple toys. We objectively measured joint attention-and the sensory-motor behaviors that underlie it-using a dual head-mounted eye-tracking system and frame-by-frame coding of manual actions. By tracking the momentary visual fixations and hand actions of each participant, we precisely determined just how often they fixated on the same object at the same time, the visual behaviors that preceded joint attention and manual behaviors that preceded and co-occurred with joint attention. We found that multiple sequential sensory-motor patterns lead to joint attention. In addition, there are developmental changes in this multi-pathway system evidenced as variations in strength among multiple routes. We propose that coordinated visual attention between parents and toddlers is primarily a sensory-motor behavior. Skill in achieving coordinated visual attention in social settings-like skills in other sensory-motor domains-emerges from multiple pathways to the same functional end. Copyright © 2016 Cognitive Science Society, Inc.

Effects of gestational length, gender, postnatal age, and birth order on visual contrast sensitivity in infants

PubMed Central

Dobkins, Karen R.; Bosworth, Rain G.; McCleery, Joseph P.

2010-01-01

To investigate effects of visual experience versus preprogrammed mechanisms on visual development, we used multiple regression analysis to determine the extent to which a variety of variables (that differ in the extent to which they are tied to visual experience) predict luminance and chromatic (red/green) contrast sensitivity (CS), which are mediated by the magnocellular (M) and parvocellular (P) subcortical pathways, respectively. Our variables included gestational length (GL), birth weight (BW), gender, postnatal age (PNA), and birth order (BO). Two-month-olds (n = 60) and 6-month-olds (n = 122) were tested. Results revealed that (1) at 2 months, infants with longer GL have higher luminance CS; (2) at both ages, CS significantly increases over a ~21-day range of PNA, but this effect is stronger in 2- than 6-month-olds and stronger for chromatic than luminance CS; (3) at 2 months, boys have higher luminance CS than girls; and (4) at 2 months, firstborn infants have higher CS, while at 6 months, non-firstborn infants have higher CS. The results for PNA/GL are consistent with the possibility that P pathway development is more influenced by variables tied to visual experience (PNA), while M pathway development is more influenced by variables unrelated to visual experience (GL). Other variables, including prenatal environment, are also discussed. PMID:19810800

Differential Expression Patterns of occ1-Related Genes in Adult Monkey Visual Cortex

PubMed Central

Takahata, Toru; Komatsu, Yusuke; Watakabe, Akiya; Hashikawa, Tsutomu; Tochitani, Shiro

2009-01-01

We have previously revealed that occ1 is preferentially expressed in the primary visual area (V1) of the monkey neocortex. In our attempt to identify more area-selective genes in the macaque neocortex, we found that testican-1, an occ1-related gene, and its family members also exhibit characteristic expression patterns along the visual pathway. The expression levels of testican-1 and testican-2 mRNAs as well as that of occ1 mRNA start of high in V1, progressively decrease along the ventral visual pathway, and end of low in the temporal areas. Complementary to them, the neuronal expression of SPARC mRNA is abundant in the association areas and scarce in V1. Whereas occ1, testican-1, and testican-2 mRNAs are preferentially distributed in thalamorecipient layers including “blobs,” SPARC mRNA expression avoids these layers. Neither SC1 nor testican-3 mRNA expression is selective to particular areas, but SC1 mRNA is abundantly observed in blobs. The expressions of occ1, testican-1, testican-2, and SC1 mRNA were downregulated after monocular tetrodotoxin injection. These results resonate with previous works on chemical and functional gradients along the primate occipitotemporal visual pathway and raise the possibility that these gradients and functional architecture may be related to the visual activity–dependent expression of these extracellular matrix glycoproteins. PMID:19073625

Flow, affect and visual creativity.

PubMed

Cseh, Genevieve M; Phillips, Louise H; Pearson, David G

2015-01-01

Flow (being in the zone) is purported to have positive consequences in terms of affect and performance; however, there is no empirical evidence about these links in visual creativity. Positive affect often--but inconsistently--facilitates creativity, and both may be linked to experiencing flow. This study aimed to determine relationships between these variables within visual creativity. Participants performed the creative mental synthesis task to simulate the creative process. Affect change (pre- vs. post-task) and flow were measured via questionnaires. The creativity of synthesis drawings was rated objectively and subjectively by judges. Findings empirically demonstrate that flow is related to affect improvement during visual creativity. Affect change was linked to productivity and self-rated creativity, but no other objective or subjective performance measures. Flow was unrelated to all external performance measures but was highly correlated with self-rated creativity; flow may therefore motivate perseverance towards eventual excellence rather than provide direct cognitive enhancement.

Inter-area correlations in the ventral visual pathway reflect feature integration

PubMed Central

Freeman, Jeremy; Donner, Tobias H.; Heeger, David J.

2011-01-01

During object perception, the brain integrates simple features into representations of complex objects. A perceptual phenomenon known as visual crowding selectively interferes with this process. Here, we use crowding to characterize a neural correlate of feature integration. Cortical activity was measured with functional magnetic resonance imaging, simultaneously in multiple areas of the ventral visual pathway (V1–V4 and the visual word form area, VWFA, which responds preferentially to familiar letters), while human subjects viewed crowded and uncrowded letters. Temporal correlations between cortical areas were lower for crowded letters than for uncrowded letters, especially between V1 and VWFA. These differences in correlation were retinotopically specific, and persisted when attention was diverted from the letters. But correlation differences were not evident when we substituted the letters with grating patches that were not crowded under our stimulus conditions. We conclude that inter-area correlations reflect feature integration and are disrupted by crowding. We propose that crowding may perturb the transformations between neural representations along the ventral pathway that underlie the integration of features into objects. PMID:21521832

Neural correlates of consciousness: a definition of the dorsal and ventral streams and their relation to phenomenology.

PubMed

Vakalopoulos, Costa

2005-01-01

The paper presents a hypothesis for a neural correlate of consciousness. A proposal is made that both the dorsal and ventral streams must be concurrently active to generate conscious awareness and that V1 (striate cortex) provides a serial link between them. An argument is presented against a true extrastriate communication between the dorsal and ventral streams. Secondly, a detailed theory is developed for the structure of the visual hierarchy. Premotor theory states that each organism-object interaction can be described by the two quantitative measures of torque and change in joint position served by the basal ganglia and cerebellum, respectively. This leads to a component theory of motor efference copy providing a fundamental tool for categorizing dorsal and ventral stream networks. The rationale for this is that the dorsal stream specifies spatial coordinates of the external world, which can be coded by the reafference of changes in joint position. The ventral stream is concerned with object recognition and is coded for by forces exerted on the world during a developmental exploratory phase of the organism. The proposed pathways for a component motor efference copy from both the cerebellum and basal ganglia converge on the thalamus and modulate thalamocortical projections via the thalamic reticular nucleus. The origin of the corticopontine projections, which are a massive pathway for cortical information to reach the cerebellum, coincides with the area typically considered as part of the dorsal stream, whereas the entire cortex projects to the striatum. This adds empirical support for a new conceptualization of the visual streams. The model also presents a solution to the binding problem of a neural correlate of consciousness, that is, how a distributed neural network synchronizes its activity during a cognitive event. It represents a reinterpretation of the current status of the visual hierarchy.

Numerical cognition is resilient to dramatic changes in early sensory experience.

PubMed

Kanjlia, Shipra; Feigenson, Lisa; Bedny, Marina

2018-06-20

Humans and non-human animals can approximate large visual quantities without counting. The approximate number representations underlying this ability are noisy, with the amount of noise proportional to the quantity being represented. Numerate humans also have access to a separate system for representing exact quantities using number symbols and words; it is this second, exact system that supports most of formal mathematics. Although numerical approximation abilities and symbolic number abilities are distinct in representational format and in their phylogenetic and ontogenetic histories, they appear to be linked throughout development--individuals who can more precisely discriminate quantities without counting are better at math. The origins of this relationship are debated. On the one hand, symbolic number abilities may be directly linked to, perhaps even rooted in, numerical approximation abilities. On the other hand, the relationship between the two systems may simply reflect their independent relationships with visual abilities. To test this possibility, we asked whether approximate number and symbolic math abilities are linked in congenitally blind individuals who have never experienced visual sets or used visual strategies to learn math. Congenitally blind and blind-folded sighted participants completed an auditory numerical approximation task, as well as a symbolic arithmetic task and non-math control tasks. We found that the precision of approximate number representations was identical across congenitally blind and sighted groups, suggesting that the development of the Approximate Number System (ANS) does not depend on visual experience. Crucially, the relationship between numerical approximation and symbolic math abilities is preserved in congenitally blind individuals. These data support the idea that the Approximate Number System and symbolic number abilities are intrinsically linked, rather than indirectly linked through visual abilities. Copyright © 2018. Published by Elsevier B.V.

Linking mechanistic data to endpoints of regulatory concern using the adverse outcome pathway framework.

EPA Science Inventory

In order to increase the uptake and use of high throughput screening data in environmental risk assessment, it is important to establish scientifically credible links between measures of biological pathway perturbation and apical adverse outcomes in humans and wildlife. The adver...

Plant Reactome: a resource for plant pathways and comparative analysis

PubMed Central

Naithani, Sushma; Preece, Justin; D'Eustachio, Peter; Gupta, Parul; Amarasinghe, Vindhya; Dharmawardhana, Palitha D.; Wu, Guanming; Fabregat, Antonio; Elser, Justin L.; Weiser, Joel; Keays, Maria; Fuentes, Alfonso Munoz-Pomer; Petryszak, Robert; Stein, Lincoln D.; Ware, Doreen; Jaiswal, Pankaj

2017-01-01

Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX. PMID:27799469

Systematic analysis of signaling pathways using an integrative environment.

PubMed

Visvanathan, Mahesh; Breit, Marc; Pfeifer, Bernhard; Baumgartner, Christian; Modre-Osprian, Robert; Tilg, Bernhard

2007-01-01

Understanding the biological processes of signaling pathways as a whole system requires an integrative software environment that has comprehensive capabilities. The environment should include tools for pathway design, visualization, simulation and a knowledge base concerning signaling pathways as one. In this paper we introduce a new integrative environment for the systematic analysis of signaling pathways. This system includes environments for pathway design, visualization, simulation and a knowledge base that combines biological and modeling information concerning signaling pathways that provides the basic understanding of the biological system, its structure and functioning. The system is designed with a client-server architecture. It contains a pathway designing environment and a simulation environment as upper layers with a relational knowledge base as the underlying layer. The TNFa-mediated NF-kB signal trans-duction pathway model was designed and tested using our integrative framework. It was also useful to define the structure of the knowledge base. Sensitivity analysis of this specific pathway was performed providing simulation data. Then the model was extended showing promising initial results. The proposed system offers a holistic view of pathways containing biological and modeling data. It will help us to perform biological interpretation of the simulation results and thus contribute to a better understanding of the biological system for drug identification.

Connectivity between the superior colliculus and the amygdala in humans and macaque monkeys: virtual dissection with probabilistic DTI tractography

PubMed Central

Koller, Kristin; Bultitude, Janet H.; Mullins, Paul; Ward, Robert; Mitchell, Anna S.; Bell, Andrew H.

2015-01-01

It has been suggested that some cortically blind patients can process the emotional valence of visual stimuli via a fast, subcortical pathway from the superior colliculus (SC) that reaches the amygdala via the pulvinar. We provide in vivo evidence for connectivity between the SC and the amygdala via the pulvinar in both humans and rhesus macaques. Probabilistic diffusion tensor imaging tractography revealed a streamlined path that passes dorsolaterally through the pulvinar before arcing rostrally to traverse above the temporal horn of the lateral ventricle and connect to the lateral amygdala. To obviate artifactual connectivity with crossing fibers of the stria terminalis, the stria was also dissected. The putative streamline between the SC and amygdala traverses above the temporal horn dorsal to the stria terminalis and is positioned medial to it in humans and lateral to it in monkeys. The topography of the streamline was examined in relation to lesion anatomy in five patients who had previously participated in behavioral experiments studying the processing of emotionally valenced visual stimuli. The pulvinar lesion interrupted the streamline in two patients who had exhibited contralesional processing deficits and spared the streamline in three patients who had no deficit. Although not definitive, this evidence supports the existence of a subcortical pathway linking the SC with the amygdala in primates. It also provides a necessary bridge between behavioral data obtained in future studies of neurological patients, and any forthcoming evidence from more invasive techniques, such as anatomical tracing studies and electrophysiological investigations only possible in nonhuman species. PMID:26224780

An OGA-Resistant Probe Allows Specific Visualization and Accurate Identification of O-GlcNAc-Modified Proteins in Cells.

PubMed

Li, Jing; Wang, Jiajia; Wen, Liuqing; Zhu, He; Li, Shanshan; Huang, Kenneth; Jiang, Kuan; Li, Xu; Ma, Cheng; Qu, Jingyao; Parameswaran, Aishwarya; Song, Jing; Zhao, Wei; Wang, Peng George

2016-11-18

O-linked β-N-acetyl-glucosamine (O-GlcNAc) is an essential and ubiquitous post-translational modification present in nucleic and cytoplasmic proteins of multicellular eukaryotes. The metabolic chemical probes such as GlcNAc or GalNAc analogues bearing ketone or azide handles, in conjunction with bioorthogonal reactions, provide a powerful approach for detecting and identifying this modification. However, these chemical probes either enter multiple glycosylation pathways or have low labeling efficiency. Therefore, selective and potent probes are needed to assess this modification. We report here the development of a novel probe, 1,3,6-tri-O-acetyl-2-azidoacetamido-2,4-dideoxy-d-glucopyranose (Ac 3 4dGlcNAz), that can be processed by the GalNAc salvage pathway and transferred by O-GlcNAc transferase (OGT) to O-GlcNAc proteins. Due to the absence of a hydroxyl group at C4, this probe is less incorporated into α/β 4-GlcNAc or GalNAc containing glycoconjugates. Furthermore, the O-4dGlcNAz modification was resistant to the hydrolysis of O-GlcNAcase (OGA), which greatly enhanced the efficiency of incorporation for O-GlcNAcylation. Combined with a click reaction, Ac 3 4dGlcNAz allowed the selective visualization of O-GlcNAc in cells and accurate identification of O-GlcNAc-modified proteins with LC-MS/MS. This probe represents a more potent and selective tool in tracking, capturing, and identifying O-GlcNAc-modified proteins in cells and cell lysates.

Variation in White Matter Connectivity Predicts the Ability to Remember Faces and Discriminate Their Emotions

PubMed Central

Unger, Ashley; Alm, Kylie H.; Collins, Jessica A.; O’Leary, Jacqueline M.; Olson, Ingrid R.

2017-01-01

Objective The extended face network contains clusters of neurons that perform distinct functions on facial stimuli. Regions in the posterior ventral visual stream appear to perform basic perceptual functions on faces, while more anterior regions, such as the ventral anterior temporal lobe and amygdala, function to link mnemonic and affective information to faces. Anterior and posterior regions are interconnected by a long-range white matter tracts however it is not known if variation in connectivity of these pathways explains cognitive performance. Methods Here, we used diffusion imaging and deterministic tractography in a cohort of 28 neurologically normal adults ages 18–28 to examine microstructural properties of visual fiber pathways and their relationship to certain mnemonic and affective functions involved in face processing. We investigated how inter-individual variability in two tracts, the inferior longitudinal fasciculus (ILF) and the inferior fronto-occipital fasciculus (IFOF), related to performance on tests of facial emotion recognition and face memory. Results Results revealed that microstructure of both tracts predicted variability in behavioral performance indexed by both tasks, suggesting that the ILF and IFOF play a role in facilitating our ability to discriminate emotional expressions in faces, as well as to remember unique faces. Variation in a control tract, the uncinate fasciculus, did not predict performance on these tasks. Conclusions These results corroborate and extend the findings of previous neuropsychology studies investigating the effects of damage to the ILF and IFOF, and demonstrate that differences in face processing abilities are related to white matter microstructure, even in healthy individuals. PMID:26888615

Two different mirror neuron networks: The sensorimotor (hand) and limbic (face) pathways.

PubMed

Ferrari, P F; Gerbella, M; Coudé, G; Rozzi, S

2017-09-01

The vast majority of functional studies investigating mirror neurons (MNs) explored their properties in relation to hand actions, and very few investigated how MNs respond to mouth actions or communicative gestures. Since hand and mouth MNs were recorded in two partially overlapping sectors of the ventral precentral cortex of the macaque monkey, there is a general assumption that they share a same neuroanatomical network, with the parietal cortex as a main source of visual information. In the current review, we challenge this perspective and describe the connectivity pattern of mouth MN sector. The mouth MNs F5/opercular region is connected with premotor, parietal areas mostly related to the somatosensory and motor representation of the face/mouth, and with area PrCO, involved in processing gustatory and somatosensory intraoral input. Unlike hand MNs, mouth MNs do not receive their visual input from parietal regions. Such information related to face/communicative behaviors could come from the ventrolateral prefrontal cortex. Further strong connections derive from limbic structures involved in encoding emotional facial expressions and motivational/reward processing. These brain structures include the anterior cingulate cortex, the anterior and mid-dorsal insula, orbitofrontal cortex and the basolateral amygdala. The mirror mechanism is therefore composed and supported by at least two different anatomical pathways: one is concerned with sensorimotor transformation in relation to reaching and hand grasping within the traditional parietal-premotor circuits; the second one is linked to the mouth/face motor control and is connected with limbic structures, involved in communication/emotions and reward processing. Copyright © 2017. Published by Elsevier Ltd.

Image and emotion: from outcomes to brain behavior.

PubMed

Nanda, Upali; Zhu, Xi; Jansen, Ben H

2012-01-01

A systematic review of neuroscience articles on the emotional states of fear, anxiety, and pain to understand how emotional response is linked to the visual characteristics of an image at the level of brain behavior. A number of outcome studies link exposure to visual images (with nature content) to improvements in stress, anxiety, and pain perception. However, an understanding of the underlying perceptual mechanisms has been lacking. In this article, neuroscience studies that use visual images to induce fear, anxiety, or pain are reviewed to gain an understanding of how the brain processes visual images in this context and to explore whether this processing can be linked to specific visual characteristics. The amygdala was identified as one of the key regions of the brain involved in the processing of fear, anxiety, and pain (induced by visual images). Other key areas included the thalamus, insula, and hippocampus. Characteristics of visual images such as the emotional dimension (valence/arousal), subject matter (familiarity, ambiguity, novelty, realism, and facial expressions), and form (sharp and curved contours) were identified as key factors influencing emotional processing. The broad structural properties of an image and overall content were found to have a more pivotal role in the emotional response than the specific details of an image. Insights on specific visual properties were translated to recommendations for what should be incorporated-and avoided-in healthcare environments.

The calcineurin pathway links hyperpolarization (Kir2.1)-induced Ca2+ signals to human myoblast differentiation and fusion.

PubMed

Konig, Stéphane; Béguet, Anne; Bader, Charles R; Bernheim, Laurent

2006-08-01

In human myoblasts triggered to differentiate, a hyperpolarization, resulting from K+ channel (Kir2.1) activation, allows the generation of an intracellular Ca2+ signal. This signal induces an increase in expression/activity of two key transcription factors of the differentiation process, myogenin and MEF2. Blocking hyperpolarization inhibits myoblast differentiation. The link between hyperpolarization-induced Ca2+ signals and the four main regulatory pathways involved in myoblast differentiation was the object of this study. Of the calcineurin, p38-MAPK, PI3K and CaMK pathways, only the calcineurin pathway was inhibited when Kir2.1-linked hyperpolarization was blocked. The CaMK pathway, although Ca2+ dependent, is unaffected by changes in membrane potential or block of Kir2.1 channels. Concerning the p38-MAPK and PI3K pathways, their activity is present already in proliferating myoblasts and they are unaffected by hyperpolarization or Kir2.1 channel block. We conclude that the Kir2.1-induced hyperpolarization triggers human myoblast differentiation via the activation of the calcineurin pathway, which, in turn, induces expression/activity of myogenin and MEF2.

Sex differences in adults' relative visual interest in female and male faces, toys, and play styles.

PubMed

Alexander, Gerianne M; Charles, Nora

2009-06-01

An individual's reproductive potential appears to influence response to attractive faces of the opposite sex. Otherwise, relatively little is known about the characteristics of the adult observer that may influence his or her affective evaluation of male and female faces. An untested hypothesis (based on the proposed role of attractive faces in mate selection) is that most women would show greater interest in male faces whereas most men would show greater interest in female faces. Further, evidence from individuals with preferences for same-sex sexual partners suggests that response to attractive male and female faces may be influenced by gender-linked play preferences. To test these hypotheses, visual attention directed to sex-linked stimuli (faces, toys, play styles) was measured in 39 men and 44 women using eye tracking technology. Consistent with our predictions, men directed greater visual attention to all male-typical stimuli and visual attention to male and female faces was associated with visual attention to gender conforming or nonconforming stimuli in a manner consistent with previous research on sexual orientation. In contrast, women showed a visual preference for female-typical toys, but no visual preference for male faces or female-typical play styles. These findings indicate that sex differences in visual processing extend beyond stimuli associated with adult sexual behavior. We speculate that sex differences in visual processing are a component of the expression of gender phenotypes across the lifespan that may reflect sex differences in the motivational properties of gender-linked stimuli.

The ‘when’ parietal pathway explored by lesion studies

PubMed Central

Battelli, Lorella; Walsh, Vincent; Pascual-Leone, Alvaro; Cavanagh, Patrick

2016-01-01

Summary The perception of events in space and time is at the root of our interactions with the environment. The precision with which we perceive visual events in time enables us to act upon objects with great accuracy and the loss of such functions, due to brain lesions can be catastrophic. We outline a visual timing mechanism that deals with the trajectory of an object’s existence across time, a critical function when keeping track of multiple objects that temporally overlap or occur sequentially. Recent evidence suggests these functions are served by an extended network of areas which we call the ‘when’ pathway. Here we show that the when pathway is distinct from and interacts with, the well established ‘where’ and ‘what’ pathways. PMID:18708141

NemaPath: online exploration of KEGG-based metabolic pathways for nematodes

PubMed Central

Wylie, Todd; Martin, John; Abubucker, Sahar; Yin, Yong; Messina, David; Wang, Zhengyuan; McCarter, James P; Mitreva, Makedonka

2008-01-01

Background Nematode.net is a web-accessible resource for investigating gene sequences from parasitic and free-living nematode genomes. Beyond the well-characterized model nematode C. elegans, over 500,000 expressed sequence tags (ESTs) and nearly 600,000 genome survey sequences (GSSs) have been generated from 36 nematode species as part of the Parasitic Nematode Genomics Program undertaken by the Genome Center at Washington University School of Medicine. However, these sequencing data are not present in most publicly available protein databases, which only include sequences in Swiss-Prot. Swiss-Prot, in turn, relies on GenBank/Embl/DDJP for predicted proteins from complete genomes or full-length proteins. Description Here we present the NemaPath pathway server, a web-based pathway-level visualization tool for navigating putative metabolic pathways for over 30 nematode species, including 27 parasites. The NemaPath approach consists of two parts: 1) a backend tool to align and evaluate nematode genomic sequences (curated EST contigs) against the annotated Kyoto Encyclopedia of Genes and Genomes (KEGG) protein database; 2) a web viewing application that displays annotated KEGG pathway maps based on desired confidence levels of primary sequence similarity as defined by a user. NemaPath also provides cross-referenced access to nematode genome information provided by other tools available on Nematode.net, including: detailed NemaGene EST cluster information; putative translations; GBrowse EST cluster views; links from nematode data to external databases for corresponding synonymous C. elegans counterparts, subject matches in KEGG's gene database, and also KEGG Ontology (KO) identification. Conclusion The NemaPath server hosts metabolic pathway mappings for 30 nematode species and is available on the World Wide Web at . The nematode source sequences used for the metabolic pathway mappings are available via FTP , as provided by the Genome Center at Washington University School of Medicine. PMID:18983679

Neuro-Ophthalmological Disorders in Cerebral Palsy: Ophthalmological, Oculomotor, and Visual Aspects

ERIC Educational Resources Information Center

Fazzi, Elisa; Signorini, Sabrina G.; La Piana, Roberta; Bertone, Chiara; Misefari, Walter; Galli, Jessica; Balottin, Umberto; Bianchi, Paolo Emilio

2012-01-01

Aim: Cerebral visual impairment (CVI) is a disorder caused by damage to the retrogeniculate visual pathways. Cerebral palsy (CP) and CVI share a common origin: 60 to 70% of children with CP also have CVI. We set out to describe visual dysfunction in children with CP. A further aim was to establish whether different types of CP are associated with…

Rapid Motion Adaptation Reveals the Temporal Dynamics of Spatiotemporal Correlation between ON and OFF Pathways

PubMed Central

Oluk, Can; Pavan, Andrea; Kafaligonul, Hulusi

2016-01-01

At the early stages of visual processing, information is processed by two major thalamic pathways encoding brightness increments (ON) and decrements (OFF). Accumulating evidence suggests that these pathways interact and merge as early as in primary visual cortex. Using regular and reverse-phi motion in a rapid adaptation paradigm, we investigated the temporal dynamics of within and across pathway mechanisms for motion processing. When the adaptation duration was short (188 ms), reverse-phi and regular motion led to similar adaptation effects, suggesting that the information from the two pathways are combined efficiently at early-stages of motion processing. However, as the adaption duration was increased to 752 ms, reverse-phi and regular motion showed distinct adaptation effects depending on the test pattern used, either engaging spatiotemporal correlation between the same or opposite contrast polarities. Overall, these findings indicate that spatiotemporal correlation within and across ON-OFF pathways for motion processing can be selectively adapted, and support those models that integrate within and across pathway mechanisms for motion processing. PMID:27667401

Evaluation of afferent pain pathways in adrenomyeloneuropathic patients.

PubMed

Yagüe, Sara; Veciana, Misericordia; Casasnovas, Carlos; Ruiz, Montserrat; Pedro, Jordi; Valls-Solé, Josep; Pujol, Aurora

2018-03-01

Patients with adrenomyeloneuropathy may have dysfunctions of visual, auditory, motor and somatosensory pathways. We thought on examining the nociceptive pathways by means of laser evoked potentials (LEPs), to obtain additional information on the pathophysiology of this condition. In 13 adrenomyeloneuropathic patients we examined LEPs to leg, arm and face stimulation. Normative data were obtained from 10 healthy subjects examined in the same experimental conditions. We also examined brainstem auditory evoked potentials (BAEPs), pattern reversal full-field visual evoked potentials (VEPs), motor evoked potentials (MEPs) and somatosensory evoked potentials (SEPs). Upper and lower limb MEPs and SEPs, as well as BAEPs, were abnormal in all patients, while VEPs were abnormal in 3 of them (23.1%). LEPs revealed abnormalities to stimulation of the face in 4 patients (30.7%), the forearm in 4 patients (30.7%) and the leg in 10 patients (76.9%). The pathologic process of adrenomyeloneuropathy is characterized by a preferential involvement of auditory, motor and somatosensory tracts and less severely of the visual and nociceptive pathways. This non-inflammatory distal axonopathy preferably damages large myelinated spinal tracts but there is also partial involvement of small myelinated fibres. LEPs studies can provide relevant information about afferent pain pathways involvement in adrenomyeloneuropathic patients. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

Changes of Visual Pathway and Brain Connectivity in Glaucoma: A Systematic Review

PubMed Central

Nuzzi, Raffaele; Dallorto, Laura; Rolle, Teresa

2018-01-01

Background: Glaucoma is a leading cause of irreversible blindness worldwide. The increasing interest in the involvement of the cortical visual pathway in glaucomatous patients is due to the implications in recent therapies, such as neuroprotection and neuroregeneration. Objective: In this review, we outline the current understanding of brain structural, functional, and metabolic changes detected with the modern techniques of neuroimaging in glaucomatous subjects. Methods: We screened MEDLINE, EMBASE, CINAHL, CENTRAL, LILACS, Trip Database, and NICE for original contributions published until 31 October 2017. Studies with at least six patients affected by any type of glaucoma were considered. We included studies using the following neuroimaging techniques: functional Magnetic Resonance Imaging (fMRI), resting-state fMRI (rs-fMRI), magnetic resonance spectroscopy (MRS), voxel- based Morphometry (VBM), surface-based Morphometry (SBM), diffusion tensor MRI (DTI). Results: Over a total of 1,901 studies, 56 case series with a total of 2,381 patients were included. Evidence of neurodegenerative process in glaucomatous patients was found both within and beyond the visual system. Structural alterations in visual cortex (mainly reduced cortex thickness and volume) have been demonstrated with SBM and VBM; these changes were not limited to primary visual cortex but also involved association visual areas. Other brain regions, associated with visual function, demonstrated a certain grade of increased or decreased gray matter volume. Functional and metabolic abnormalities resulted within primary visual cortex in all studies with fMRI and MRS. Studies with rs-fMRI found disrupted connectivity between the primary and higher visual cortex and between visual cortex and associative visual areas in the task-free state of glaucomatous patients. Conclusions: This review contributes to the better understanding of brain abnormalities in glaucoma. It may stimulate further speculation about brain plasticity at a later age and therapeutic strategies, such as the prevention of cortical degeneration in patients with glaucoma. Structural, functional, and metabolic neuroimaging methods provided evidence of changes throughout the visual pathway in glaucomatous patients. Other brain areas, not directly involved in the processing of visual information, also showed alterations. PMID:29896087

The Location of Sources of Human Computer Processed Cerebral Potentials for the Automated Assessment of Visual Field Impairment

PubMed Central

Leisman, Gerald; Ashkenazi, Maureen

1979-01-01

Objective psychophysical techniques for investigating visual fields are described. The paper concerns methods for the collection and analysis of evoked potentials using a small laboratory computer and provides efficient methods for obtaining information about the conduction pathways of the visual system.

Learning Visual Design through Hypermedia: Pathways to Visual Literacy.

ERIC Educational Resources Information Center

Lockee, Barbara; Hergert, Tom

The interactive multimedia application described here attempts to provide learners and teachers with a common frame of reference for communicating about visual media. The system is based on a list of concepts related to composition, and illustrates those concepts with photographs, paintings, graphic designs, and motion picture scenes. The ability…

Migration Pathways of Thalamic Neurons and Development of Thalamocortical Connections in Humans Revealed by Diffusion MR Tractography.

PubMed

Wilkinson, Molly; Kane, Tara; Wang, Rongpin; Takahashi, Emi

2017-12-01

The thalamus plays an important role in signal relays in the brain, with thalamocortical (TC) neuronal pathways linked to various sensory/cognitive functions. In this study, we aimed to see fetal and postnatal development of the thalamus including neuronal migration to the thalamus and the emergence/maturation of the TC pathways. Pathways from/to the thalami of human postmortem fetuses and in vivo subjects ranging from newborns to adults with no neurological histories were studied using high angular resolution diffusion MR imaging (HARDI) tractography. Pathways likely linked to neuronal migration from the ventricular zone and ganglionic eminence (GE) to the thalami were both successfully detected. Between the ventricular zone and thalami, more tractography pathways were found in anterior compared with posterior regions, which was well in agreement with postnatal observations that the anterior TC segment had more tract count and volume than the posterior segment. Three different pathways likely linked to neuronal migration from the GE to the thalami were detected. No hemispheric asymmetry of the TC pathways was quantitatively observed during development. These results suggest that HARDI tractography is useful to identify multiple differential neuronal migration pathways in human brains, and regional differences in brain development in fetal ages persisted in postnatal development. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The sequence of cortical activity inferred by response latency variability in the human ventral pathway of face processing.

PubMed

Lin, Jo-Fu Lotus; Silva-Pereyra, Juan; Chou, Chih-Che; Lin, Fa-Hsuan

2018-04-11

Variability in neuronal response latency has been typically considered caused by random noise. Previous studies of single cells and large neuronal populations have shown that the temporal variability tends to increase along the visual pathway. Inspired by these previous studies, we hypothesized that functional areas at later stages in the visual pathway of face processing would have larger variability in the response latency. To test this hypothesis, we used magnetoencephalographic data collected when subjects were presented with images of human faces. Faces are known to elicit a sequence of activity from the primary visual cortex to the fusiform gyrus. Our results revealed that the fusiform gyrus showed larger variability in the response latency compared to the calcarine fissure. Dynamic and spectral analyses of the latency variability indicated that the response latency in the fusiform gyrus was more variable than in the calcarine fissure between 70 ms and 200 ms after the stimulus onset and between 4 Hz and 40 Hz, respectively. The sequential processing of face information from the calcarine sulcus to the fusiform sulcus was more reliably detected based on sizes of the response variability than instants of the maximal response peaks. With two areas in the ventral visual pathway, we show that the variability in response latency across brain areas can be used to infer the sequence of cortical activity.

Dynamic circuitry for updating spatial representations. II. Physiological evidence for interhemispheric transfer in area LIP of the split-brain macaque.

PubMed

Heiser, Laura M; Berman, Rebecca A; Saunders, Richard C; Colby, Carol L

2005-11-01

With each eye movement, a new image impinges on the retina, yet we do not notice any shift in visual perception. This perceptual stability indicates that the brain must be able to update visual representations to take our eye movements into account. Neurons in the lateral intraparietal area (LIP) update visual representations when the eyes move. The circuitry that supports these updated representations remains unknown, however. In this experiment, we asked whether the forebrain commissures are necessary for updating in area LIP when stimulus representations must be updated from one visual hemifield to the other. We addressed this question by recording from LIP neurons in split-brain monkeys during two conditions: stimulus traces were updated either across or within hemifields. Our expectation was that across-hemifield updating activity in LIP would be reduced or abolished after transection of the forebrain commissures. Our principal finding is that LIP neurons can update stimulus traces from one hemifield to the other even in the absence of the forebrain commissures. This finding provides the first evidence that representations in parietal cortex can be updated without the use of direct cortico-cortical links. The second main finding is that updating activity in LIP is modified in the split-brain monkey: across-hemifield signals are reduced in magnitude and delayed in onset compared with within-hemifield signals, which indicates that the pathways for across-hemifield updating are less effective in the absence of the forebrain commissures. Together these findings reveal a dynamic circuit that contributes to updating spatial representations.

Asymmetric top-down modulation of ascending visual pathways in pigeons.

PubMed

Freund, Nadja; Valencia-Alfonso, Carlos E; Kirsch, Janina; Brodmann, Katja; Manns, Martina; Güntürkün, Onur

2016-03-01

Cerebral asymmetries are a ubiquitous phenomenon evident in many species, incl. humans, and they display some similarities in their organization across vertebrates. In many species the left hemisphere is associated with the ability to categorize objects based on abstract or experience-based behaviors. Using the asymmetrically organized visual system of pigeons as an animal model, we show that descending forebrain pathways asymmetrically modulate visually evoked responses of single thalamic units. Activity patterns of neurons within the nucleus rotundus, the largest thalamic visual relay structure in birds, were differently modulated by left and right hemispheric descending systems. Thus, visual information ascending towards the left hemisphere was modulated by forebrain top-down systems at thalamic level, while right thalamic units were strikingly less modulated. This asymmetry of top-down control could promote experience-based processes within the left hemisphere, while biasing the right side towards stimulus-bound response patterns. In a subsequent behavioral task we tested the possible functional impact of this asymmetry. Under monocular conditions, pigeons learned to discriminate color pairs, so that each hemisphere was trained on one specific discrimination. Afterwards the animals were presented with stimuli that put the hemispheres in conflict. Response patterns on the conflicting stimuli revealed a clear dominance of the left hemisphere. Transient inactivation of left hemispheric top-down control reduced this dominance while inactivation of right hemispheric top-down control had no effect on response patterns. Functional asymmetries of descending systems that modify visual ascending pathways seem to play an important role in the superiority of the left hemisphere in experience-based visual tasks. Copyright © 2015. Published by Elsevier Ltd.

Are patients with Parkinson’s disease blind to blindsight?

PubMed Central

Stebbins, Glenn; Schiltz, Christine; Goetz, Christopher G.

2014-01-01

In Parkinson’s disease, visual dysfunction is prominent. Visual hallucinations can be a major hallmark of late stage disease, but numerous visual deficits also occur in early stage Parkinson’s disease. Specific retinopathy, deficits in the primary visual pathway and the secondary ventral and dorsal pathways, as well as dysfunction of the attention pathways have all been posited as causes of hallucinations in Parkinson’s disease. We present data from patients with Parkinson’s disease that contrast with a known neuro-ophthalmological syndrome, termed ‘blindsight’. In this syndrome, there is an absence of conscious object identification, but preserved ‘guess’ of the location of a stimulus, preserved reflexive saccades and motion perception and preserved autonomical and expressive reactions to negative emotional facial expressions. We propose that patients with Parkinson’s disease have the converse of blindsight, being ‘blind to blindsight’. As such they preserve conscious vision, but show erroneous ‘guess’ localization of visual stimuli, poor saccades and motion perception, and poor emotional face perception with blunted autonomic reaction. Although a large data set on these deficits in Parkinson’s disease has been accumulated, consolidation into one specific syndrome has not been proposed. Focusing on neuropathological and physiological data from two phylogenetically old and subconscious pathways, the retino-colliculo-thalamo-amygdala and the retino-geniculo-extrastriate pathways, we propose that aberrant function of these systems, including pathologically inhibited superior colliculus activity, deficient corollary discharges to the frontal eye fields, dysfunctional pulvinar, claustrum and amygdaloid subnuclei of the amygdala, the latter progressively burdened with Lewy bodies, underlie this syndrome. These network impairments are further corroborated by the concept of the ‘silent amygdala’. Functionally being ‘blind to blindsight’ may facilitate the highly distinctive ‘presence’ or ‘passage’ hallucinations of Parkinson’s disease and can help to explain handicaps in driving capacities and dysfunctional ‘theory of mind’. We propose this synthesis to prompt refined neuropathological and neuroimaging studies on the pivotal nuclei in these pathways in order to better understand the networks underpinning this newly conceptualized syndrome in Parkinson’s disease. PMID:24764573

Crosstalk of Autophagy and the Secretory Pathway and Its Role in Diseases.

PubMed

Zahoor, Muhammad; Farhan, Hesso

2018-01-01

The secretory and autophagic pathways are two fundamental, evolutionary highly conserved endomembrane processes. Typically, secretion is associated with biosynthesis and delivery of proteins. In contrast, autophagy is usually considered as a degradative pathway. Thus, an analogy to metabolic pathways is evident. Anabolic (biosynthetic) and catabolic (degradative) pathways are usually intimately linked and intertwined, and likewise, the secretory and autophagy pathways are intertwined. Investigation of this link is an emerging area of research, and we will provide an overview of some of the major advances that have been made to contribute to understanding of how secretion regulates autophagy and vice versa. Finally, we will highlight evidence that supports a potential involvement of the autophagy-secretion crosstalk in human diseases. © 2018 Elsevier Inc. All rights reserved.

Linking Family Economic Hardship to Early Childhood Health: An Investigation of Mediating Pathways.

PubMed

Hsu, Hui-Chin; Wickrama, Kandauda A S

2015-12-01

The underlying mechanisms through which family economic adversity influences child health are less understood. Taking a process-oriented approach, this study examined maternal mental health and investment in children, child health insurance, and child healthcare as mediators linking family economic hardship (FEH) to child health. A structural equation modeling was applied to test the hypothesized mediating model. After adjustment for sociodemographic risk factors, results revealed: (1) a significant direct path linking FEH to poor child health (effect size = .372), and (2) six significant mediating pathways (total effect size = .089). In two mediating pathways, exposures to FEH undermined mothers' mental health: in the first pathway poor maternal mental health led to decreased parental investment, which, in turn, contributed to poor child health, whereas in the second pathway the adverse effect of poor maternal mental health was cascaded through child unmet healthcare need, which resulted in poor child health. One pathway involved child insurance status, where the effect of FEH increased the likelihood to be uninsured, which led to unmet healthcare need, and, in turn, to poor health. Three pathways involved preventive care: in one pathway FEH contributed to poor preventive care, which led to unmet healthcare need and then to poor health; in the other two pathways where poor preventive care respectively gave rise to decreased investment in children or poor maternal mental health, which further contributed to poor child health. Results suggest that the association between FEH and children's health is mediated by multiple pathways.

PathVisio 3: an extendable pathway analysis toolbox.

PubMed

Kutmon, Martina; van Iersel, Martijn P; Bohler, Anwesha; Kelder, Thomas; Nunes, Nuno; Pico, Alexander R; Evelo, Chris T

2015-02-01

PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to describe the detailed steps in biological processes. Those powerful, visual representations help researchers to better understand, share and discuss knowledge. Since the first publication of PathVisio in 2008, the original paper was cited more than 170 times and PathVisio was used in many different biological studies. As an online editor PathVisio is also integrated in the community curated pathway database WikiPathways. Here we present the third version of PathVisio with the newest additions and improvements of the application. The core features of PathVisio are pathway drawing, advanced data visualization and pathway statistics. Additionally, PathVisio 3 introduces a new powerful extension systems that allows other developers to contribute additional functionality in form of plugins without changing the core application. PathVisio can be downloaded from http://www.pathvisio.org and in 2014 PathVisio 3 has been downloaded over 5,500 times. There are already more than 15 plugins available in the central plugin repository. PathVisio is a freely available, open-source tool published under the Apache 2.0 license (http://www.apache.org/licenses/LICENSE-2.0). It is implemented in Java and thus runs on all major operating systems. The code repository is available at http://svn.bigcat.unimaas.nl/pathvisio. The support mailing list for users is available on https://groups.google.com/forum/#!forum/wikipathways-discuss and for developers on https://groups.google.com/forum/#!forum/wikipathways-devel.

Experience-Related Structural Changes of Degenerated Occipital White Matter in Late-Blind Humans – A Diffusion Tensor Imaging Study

PubMed Central

Dietrich, Susanne; Hertrich, Ingo; Kumar, Vinod; Ackermann, Hermann

2015-01-01

Late-blind humans can learn to understand speech at ultra-fast syllable rates (ca. 20 syllables/s), a capability associated with hemodynamic activation of the central-visual system. Thus, the observed functional cross-modal recruitment of occipital cortex might facilitate ultra-fast speech processing in these individuals. To further elucidate the structural prerequisites of this skill, diffusion tensor imaging (DTI) was conducted in late-blind subjects differing in their capability of understanding ultra-fast speech. Fractional anisotropy (FA) was determined as a quantitative measure of the directionality of water diffusion, indicating fiber tract characteristics that might be influenced by blindness as well as the acquired perceptual skills. Analysis of the diffusion images revealed reduced FA in late-blind individuals relative to sighted controls at the level of the optic radiations at either side and the right-hemisphere dorsal thalamus (pulvinar). Moreover, late-blind subjects showed significant positive correlations between FA and the capacity of ultra-fast speech comprehension within right-hemisphere optic radiation and thalamus. Thus, experience-related structural alterations occurred in late-blind individuals within visual pathways that, presumably, are linked to higher order frontal language areas. PMID:25830371

Visualizing redox orbitals and their potentials in advanced lithium-ion battery materials using high-resolution x-ray Compton scattering

PubMed Central

Hafiz, Hasnain; Suzuki, Kosuke; Barbiellini, Bernardo; Orikasa, Yuki; Callewaert, Vincent; Kaprzyk, Staszek; Itou, Masayoshi; Yamamoto, Kentaro; Yamada, Ryota; Uchimoto, Yoshiharu; Sakurai, Yoshiharu; Sakurai, Hiroshi; Bansil, Arun

2017-01-01

Reduction-oxidation (redox) reactions are the key processes that underlie the batteries powering smartphones, laptops, and electric cars. A redox process involves transfer of electrons between two species. For example, in a lithium-ion battery, current is generated when conduction electrons from the lithium anode are transferred to the redox orbitals of the cathode material. The ability to visualize or image the redox orbitals and how these orbitals evolve under lithiation and delithiation processes is thus of great fundamental and practical interest for understanding the workings of battery materials. We show that inelastic scattering spectroscopy using high-energy x-ray photons (Compton scattering) can yield faithful momentum space images of the redox orbitals by considering lithium iron phosphate (LiFePO4 or LFP) as an exemplar cathode battery material. Our analysis reveals a new link between voltage and the localization of transition metal 3d orbitals and provides insight into the puzzling mechanism of potential shift and how it is connected to the modification of the bond between the transition metal and oxygen atoms. Our study thus opens a novel spectroscopic pathway for improving the performance of battery materials. PMID:28845452

Visualizing redox orbitals and their potentials in advanced lithium-ion battery materials using high-resolution x-ray Compton scattering.

PubMed

Hafiz, Hasnain; Suzuki, Kosuke; Barbiellini, Bernardo; Orikasa, Yuki; Callewaert, Vincent; Kaprzyk, Staszek; Itou, Masayoshi; Yamamoto, Kentaro; Yamada, Ryota; Uchimoto, Yoshiharu; Sakurai, Yoshiharu; Sakurai, Hiroshi; Bansil, Arun

2017-08-01

Reduction-oxidation (redox) reactions are the key processes that underlie the batteries powering smartphones, laptops, and electric cars. A redox process involves transfer of electrons between two species. For example, in a lithium-ion battery, current is generated when conduction electrons from the lithium anode are transferred to the redox orbitals of the cathode material. The ability to visualize or image the redox orbitals and how these orbitals evolve under lithiation and delithiation processes is thus of great fundamental and practical interest for understanding the workings of battery materials. We show that inelastic scattering spectroscopy using high-energy x-ray photons (Compton scattering) can yield faithful momentum space images of the redox orbitals by considering lithium iron phosphate (LiFePO 4 or LFP) as an exemplar cathode battery material. Our analysis reveals a new link between voltage and the localization of transition metal 3d orbitals and provides insight into the puzzling mechanism of potential shift and how it is connected to the modification of the bond between the transition metal and oxygen atoms. Our study thus opens a novel spectroscopic pathway for improving the performance of battery materials.

Visual Stress in Adults with and without Dyslexia

ERIC Educational Resources Information Center

Singleton, Chris; Trotter, Susannah

2005-01-01

The relationship between dyslexia and visual stress (sometimes known as Meares-Irlen syndrome) is uncertain. While some theorists have hypothesised an aetiological link between the two conditions, mediated by the magnocellular visual system, at the present time the predominant theories of dyslexia and visual stress see them as distinct, unrelated…

Sensitivity and integration in a visual pathway for circadian entrainment in the hamster (Mesocricetus auratus).

PubMed Central

Nelson, D E; Takahashi, J S

1991-01-01

1. Light-induced phase shifts of the circadian rhythm of wheel-running activity were used to measure the photic sensitivity of a circadian pacemaker and the visual pathway that conveys light information to it in the golden hamster (Mesocricetus auratus). The sensitivity to stimulus irradiance and duration was assessed by measuring the magnitude of phase-shift responses to photic stimuli of different irradiance and duration. The visual sensitivity was also measured at three different phases of the circadian rhythm. 2. The stimulus-response curves measured at different circadian phases suggest that the maximum phase-shift is the only aspect of visual responsivity to change as a function of the circadian day. The half-saturation constants (sigma) for the stimulus-response curves are not significantly different over the three circadian phases tested. The photic sensitivity to irradiance (1/sigma) appears to remain constant over the circadian day. 3. The hamster circadian pacemaker and the photoreceptive system that subserves it are more sensitive to the irradiance of longer-duration stimuli than to irradiance of briefer stimuli. The system is maximally sensitive to the irradiance of stimuli of 300 s and longer in duration. A quantitative model is presented to explain the changes that occur in the stimulus-response curves as a function of photic stimulus duration. 4. The threshold for photic stimulation of the hamster circadian pacemaker is also quite high. The threshold irradiance (the minimum irradiance necessary to induce statistically significant responses) is approximately 10(11) photons cm-2 s-1 for optimal stimulus durations. This threshold is equivalent to a luminance at the cornea of 0.1 cd m-2. 5. We also measured the sensitivity of this visual pathway to the total number of photons in a stimulus. This system is maximally sensitive to photons in stimuli between 30 and 3600 s in duration. The maximum quantum efficiency of photic integration occurs in 300 s stimuli. 6. These results suggest that the visual pathways that convey light information to the mammalian circadian pacemaker possess several unique characteristics. These pathways are relatively insensitive to light irradiance and also integrate light inputs over relatively long durations. This visual system, therefore, possesses an optimal sensitivity of 'tuning' to total photons delivered in stimuli of several minutes in duration. Together these characteristics may make this visual system unresponsive to environmental 'noise' that would interfere with the entrainment of circadian rhythms to light-dark cycles. PMID:1895235

GABA predicts visual intelligence.

PubMed

Cook, Emily; Hammett, Stephen T; Larsson, Jonas

2016-10-06

Early psychological researchers proposed a link between intelligence and low-level perceptual performance. It was recently suggested that this link is driven by individual variations in the ability to suppress irrelevant information, evidenced by the observation of strong correlations between perceptual surround suppression and cognitive performance. However, the neural mechanisms underlying such a link remain unclear. A candidate mechanism is neural inhibition by gamma-aminobutyric acid (GABA), but direct experimental support for GABA-mediated inhibition underlying suppression is inconsistent. Here we report evidence consistent with a global suppressive mechanism involving GABA underlying the link between sensory performance and intelligence. We measured visual cortical GABA concentration, visuo-spatial intelligence and visual surround suppression in a group of healthy adults. Levels of GABA were strongly predictive of both intelligence and surround suppression, with higher levels of intelligence associated with higher levels of GABA and stronger surround suppression. These results indicate that GABA-mediated neural inhibition may be a key factor determining cognitive performance and suggests a physiological mechanism linking surround suppression and intelligence. Copyright © 2016 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

How To Produce Linked Audio and Still Visual Materials. Teaching and Learning in Higher Education, 16.

ERIC Educational Resources Information Center

Ellington, Henry

A sequel to the booklet "A Review of the Different Types of Instructional Materials Available to Teachers and Lecturers," this booklet begins by looking at the various ways in which linked audio and still visual materials can be used in different instructional situations, i.e., mass instruction, individualized learning, and group learning. Some of…

A cortical pathway to olfactory naming: evidence from primary progressive aphasia

PubMed Central

Rogalski, Emily; Harrison, Theresa; Mesulam, M.-Marsel; Gottfried, Jay A.

2013-01-01

It is notoriously difficult to name odours. Without the benefit of non-olfactory information, even common household smells elude our ability to name them. The neuroscientific basis for this olfactory language ‘deficit’ is poorly understood, and even basic models to explain how odour inputs gain access to transmodal representations required for naming have not been put forward. This study used patients with primary progressive aphasia, a clinical dementia syndrome characterized by primary deficits in language, to investigate the interactions between olfactory inputs and lexical access by assessing behavioural performance of olfactory knowledge and its relationship to brain atrophy. We specifically hypothesized that the temporal pole would play a key role in linking odour object representations to transmodal networks, given its anatomical proximity to olfactory and visual object processing areas. Behaviourally, patients with primary progressive aphasia with non-semantic subtypes were severely impaired on an odour naming task, in comparison with an age-matched control group. However, with the availability of picture cues or word cues, odour matching performance approached control levels, demonstrating an inability to retrieve but not to recognize the name and nature of the odorant. The magnitude of cortical thinning in the temporal pole was found to correlate with reductions in odour familiarity and odour matching to visual cues, whereas the inferior frontal gyrus correlated with both odour naming and matching. Volumetric changes in the mediodorsal thalamus correlated with the proportion of categorical mismatch errors, indicating a possible role of this region in error-signal monitoring to optimize recognition of associations linked to the odour. A complementary analysis of patients with the semantic subtype of primary progressive aphasia, which is associated with marked temporopolar atrophy, revealed much more pronounced impairments of odour naming and matching. In identifying the critical role of the temporal pole and inferior frontal gyrus in transmodal linking and verbalization of olfactory objects, our findings provide a new neurobiological foundation for understanding why even common odours are hard to name. PMID:23471695

Irinotecan in Treating Children With Refractory Solid Tumors

ClinicalTrials.gov

2013-06-13

Childhood Central Nervous System Germ Cell Tumor; Childhood Choroid Plexus Tumor; Childhood Craniopharyngioma; Childhood Grade I Meningioma; Childhood Grade II Meningioma; Childhood Grade III Meningioma; Childhood Infratentorial Ependymoma; Childhood Oligodendroglioma; Childhood Supratentorial Ependymoma; Previously Treated Childhood Rhabdomyosarcoma; Recurrent Childhood Cerebellar Astrocytoma; Recurrent Childhood Cerebral Astrocytoma; Recurrent Childhood Ependymoma; Recurrent Childhood Medulloblastoma; Recurrent Childhood Rhabdomyosarcoma; Recurrent Childhood Visual Pathway and Hypothalamic Glioma; Recurrent Childhood Visual Pathway Glioma; Recurrent Ewing Sarcoma/Peripheral Primitive Neuroectodermal Tumor; Recurrent Neuroblastoma; Recurrent Osteosarcoma; Unspecified Childhood Solid Tumor, Protocol Specific

PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data.

PubMed

Hart, Steven N; Moore, Raymond M; Zimmermann, Michael T; Oliver, Gavin R; Egan, Jan B; Bryce, Alan H; Kocher, Jean-Pierre A

2015-01-01

Objective. Bringing together genomics, transcriptomics, proteomics, and other -omics technologies is an important step towards developing highly personalized medicine. However, instrumentation has advances far beyond expectations and now we are able to generate data faster than it can be interpreted. Materials and Methods. We have developed PANDA (Pathway AND Annotation) Explorer, a visualization tool that integrates gene-level annotation in the context of biological pathways to help interpret complex data from disparate sources. PANDA is a web-based application that displays data in the context of well-studied pathways like KEGG, BioCarta, and PharmGKB. PANDA represents data/annotations as icons in the graph while maintaining the other data elements (i.e., other columns for the table of annotations). Custom pathways from underrepresented diseases can be imported when existing data sources are inadequate. PANDA also allows sharing annotations among collaborators. Results. In our first use case, we show how easy it is to view supplemental data from a manuscript in the context of a user's own data. Another use-case is provided describing how PANDA was leveraged to design a treatment strategy from the somatic variants found in the tumor of a patient with metastatic sarcomatoid renal cell carcinoma. Conclusion. PANDA facilitates the interpretation of gene-centric annotations by visually integrating this information with context of biological pathways. The application can be downloaded or used directly from our website: http://bioinformaticstools.mayo.edu/research/panda-viewer/.

SignaLink 2 – a signaling pathway resource with multi-layered regulatory networks

PubMed Central

2013-01-01

Background Signaling networks in eukaryotes are made up of upstream and downstream subnetworks. The upstream subnetwork contains the intertwined network of signaling pathways, while the downstream regulatory part contains transcription factors and their binding sites on the DNA as well as microRNAs and their mRNA targets. Currently, most signaling and regulatory databases contain only a subsection of this network, making comprehensive analyses highly time-consuming and dependent on specific data handling expertise. The need for detailed mapping of signaling systems is also supported by the fact that several drug development failures were caused by undiscovered cross-talk or regulatory effects of drug targets. We previously created a uniformly curated signaling pathway resource, SignaLink, to facilitate the analysis of pathway cross-talks. Here, we present SignaLink 2, which significantly extends the coverage and applications of its predecessor. Description We developed a novel concept to integrate and utilize different subsections (i.e., layers) of the signaling network. The multi-layered (onion-like) database structure is made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The user-friendly website allows the interactive exploration of how each signaling protein is regulated. The customizable download page enables the analysis of any user-specified part of the signaling network. Compared to other signaling resources, distinctive features of SignaLink 2 are the following: 1) it involves experimental data not only from humans but from two invertebrate model organisms, C. elegans and D. melanogaster; 2) combines manual curation with large-scale datasets; 3) provides confidence scores for each interaction; 4) operates a customizable download page with multiple file formats (e.g., BioPAX, Cytoscape, SBML). Non-profit users can access SignaLink 2 free of charge at http://SignaLink.org. Conclusions With SignaLink 2 as a single resource, users can effectively analyze signaling pathways, scaffold proteins, modifier enzymes, transcription factors and miRNAs that are important in the regulation of signaling processes. This integrated resource allows the systems-level examination of how cross-talks and signaling flow are regulated, as well as provide data for cross-species comparisons and drug discovery analyses. PMID:23331499

SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks.

PubMed

Fazekas, Dávid; Koltai, Mihály; Türei, Dénes; Módos, Dezső; Pálfy, Máté; Dúl, Zoltán; Zsákai, Lilian; Szalay-Bekő, Máté; Lenti, Katalin; Farkas, Illés J; Vellai, Tibor; Csermely, Péter; Korcsmáros, Tamás

2013-01-18

Signaling networks in eukaryotes are made up of upstream and downstream subnetworks. The upstream subnetwork contains the intertwined network of signaling pathways, while the downstream regulatory part contains transcription factors and their binding sites on the DNA as well as microRNAs and their mRNA targets. Currently, most signaling and regulatory databases contain only a subsection of this network, making comprehensive analyses highly time-consuming and dependent on specific data handling expertise. The need for detailed mapping of signaling systems is also supported by the fact that several drug development failures were caused by undiscovered cross-talk or regulatory effects of drug targets. We previously created a uniformly curated signaling pathway resource, SignaLink, to facilitate the analysis of pathway cross-talks. Here, we present SignaLink 2, which significantly extends the coverage and applications of its predecessor. We developed a novel concept to integrate and utilize different subsections (i.e., layers) of the signaling network. The multi-layered (onion-like) database structure is made up of signaling pathways, their pathway regulators (e.g., scaffold and endocytotic proteins) and modifier enzymes (e.g., phosphatases, ubiquitin ligases), as well as transcriptional and post-transcriptional regulators of all of these components. The user-friendly website allows the interactive exploration of how each signaling protein is regulated. The customizable download page enables the analysis of any user-specified part of the signaling network. Compared to other signaling resources, distinctive features of SignaLink 2 are the following: 1) it involves experimental data not only from humans but from two invertebrate model organisms, C. elegans and D. melanogaster; 2) combines manual curation with large-scale datasets; 3) provides confidence scores for each interaction; 4) operates a customizable download page with multiple file formats (e.g., BioPAX, Cytoscape, SBML). Non-profit users can access SignaLink 2 free of charge at http://SignaLink.org. With SignaLink 2 as a single resource, users can effectively analyze signaling pathways, scaffold proteins, modifier enzymes, transcription factors and miRNAs that are important in the regulation of signaling processes. This integrated resource allows the systems-level examination of how cross-talks and signaling flow are regulated, as well as provide data for cross-species comparisons and drug discovery analyses.

Organization and integration of biomedical knowledge with concept maps for key peroxisomal pathways.

PubMed

Willemsen, A M; Jansen, G A; Komen, J C; van Hooff, S; Waterham, H R; Brites, P M T; Wanders, R J A; van Kampen, A H C

2008-08-15

One important area of clinical genomics research involves the elucidation of molecular mechanisms underlying (complex) disorders which eventually may lead to new diagnostic or drug targets. To further advance this area of clinical genomics one of the main challenges is the acquisition and integration of data, information and expert knowledge for specific biomedical domains and diseases. Currently the required information is not very well organized but scattered over biological and biomedical databases, basic text books, scientific literature and experts' minds and may be highly specific, heterogeneous, complex and voluminous. We present a new framework to construct knowledge bases with concept maps for presentation of information and the web ontology language OWL for the representation of information. We demonstrate this framework through the construction of a peroxisomal knowledge base, which focuses on four key peroxisomal pathways and several related genetic disorders. All 155 concept maps in our knowledge base are linked to at least one other concept map, which allows the visualization of one big network of related pieces of information. The peroxisome knowledge base is available from www.bioinformaticslaboratory.nl (Support-->Web applications). Supplementary data is available from www.bioinformaticslaboratory.nl (Research-->Output--> Publications--> KB_SuppInfo)

"When the skies fight": HIV, violence and pathways of precarity in South Africa.

PubMed

Mills, Elizabeth

2016-05-01

Based on multi-sited ethnographic fieldwork in South Africa, this article explores the skies that fight, the proverbial lightning strikes that bring HIV into women's lives and bodies. Departing from earlier studies on ARV programmes in and beyond South Africa, and broadening out to explore the chronic struggle for life in a context of entrenched socio-economic inequality, this article presents findings on women's embodiment of and strategic resistance to structural and interpersonal violence. These linked forms of violence are discussed in light of the concept of precarity. Across two sections, the findings trace the pathways through which precarity entered women's lives, drawing on verbal, visual and written accounts collected through participant observation, participatory photography and film, and journey mapping. In doing so, the ethnography articulates the intersection of structural and interpersonal violence in women's lives. It also reveals the extent to which women exert a 'constrained agency', on the one hand, to resist structural violence and reconfigure their political relationship with the state through health activism; and, on the other hand, to shift the gender dynamics that fuel interpersonal violence through a careful navigation of intimacy and independence. Copyright © 2016 Elsevier Inc. All rights reserved.

P-Finder: Reconstruction of Signaling Networks from Protein-Protein Interactions and GO Annotations.

PubMed

Young-Rae Cho; Yanan Xin; Speegle, Greg

2015-01-01

Because most complex genetic diseases are caused by defects of cell signaling, illuminating a signaling cascade is essential for understanding their mechanisms. We present three novel computational algorithms to reconstruct signaling networks between a starting protein and an ending protein using genome-wide protein-protein interaction (PPI) networks and gene ontology (GO) annotation data. A signaling network is represented as a directed acyclic graph in a merged form of multiple linear pathways. An advanced semantic similarity metric is applied for weighting PPIs as the preprocessing of all three methods. The first algorithm repeatedly extends the list of nodes based on path frequency towards an ending protein. The second algorithm repeatedly appends edges based on the occurrence of network motifs which indicate the link patterns more frequently appearing in a PPI network than in a random graph. The last algorithm uses the information propagation technique which iteratively updates edge orientations based on the path strength and merges the selected directed edges. Our experimental results demonstrate that the proposed algorithms achieve higher accuracy than previous methods when they are tested on well-studied pathways of S. cerevisiae. Furthermore, we introduce an interactive web application tool, called P-Finder, to visualize reconstructed signaling networks.

The Coordination Dynamics of Observational Learning: Relative Motion Direction and Relative Phase as Informational Content Linking Action-Perception to Action-Production.

PubMed

Buchanan, John J

2016-01-01

The primary goal of this chapter is to merge together the visual perception perspective of observational learning and the coordination dynamics theory of pattern formation in perception and action. Emphasis is placed on identifying movement features that constrain and inform action-perception and action-production processes. Two sources of visual information are examined, relative motion direction and relative phase. The visual perception perspective states that the topological features of relative motion between limbs and joints remains invariant across an actor's motion and therefore are available for pickup by an observer. Relative phase has been put forth as an informational variable that links perception to action within the coordination dynamics theory. A primary assumption of the coordination dynamics approach is that environmental information is meaningful only in terms of the behavior it modifies. Across a series of single limb tasks and bimanual tasks it is shown that the relative motion and relative phase between limbs and joints is picked up through visual processes and supports observational learning of motor skills. Moreover, internal estimations of motor skill proficiency and competency are linked to the informational content found in relative motion and relative phase. Thus, the chapter links action to perception and vice versa and also links cognitive evaluations to the coordination dynamics that support action-perception and action-production processes.

Testing the generality of the zoom-lens model: Evidence for visual-pathway specific effects of attended-region size on perception.

PubMed

Goodhew, Stephanie C; Lawrence, Rebecca K; Edwards, Mark

2017-05-01

There are volumes of information available to process in visual scenes. Visual spatial attention is a critically important selection mechanism that prevents these volumes from overwhelming our visual system's limited-capacity processing resources. We were interested in understanding the effect of the size of the attended area on visual perception. The prevailing model of attended-region size across cognition, perception, and neuroscience is the zoom-lens model. This model stipulates that the magnitude of perceptual processing enhancement is inversely related to the size of the attended region, such that a narrow attended-region facilitates greater perceptual enhancement than a wider region. Yet visual processing is subserved by two major visual pathways (magnocellular and parvocellular) that operate with a degree of independence in early visual processing and encode contrasting visual information. Historically, testing of the zoom-lens has used measures of spatial acuity ideally suited to parvocellular processing. This, therefore, raises questions about the generality of the zoom-lens model to different aspects of visual perception. We found that while a narrow attended-region facilitated spatial acuity and the perception of high spatial frequency targets, it had no impact on either temporal acuity or the perception of low spatial frequency targets. This pattern also held up when targets were not presented centrally. This supports the notion that visual attended-region size has dissociable effects on magnocellular versus parvocellular mediated visual processing.

Plant Reactome: a resource for plant pathways and comparative analysis.

PubMed

Naithani, Sushma; Preece, Justin; D'Eustachio, Peter; Gupta, Parul; Amarasinghe, Vindhya; Dharmawardhana, Palitha D; Wu, Guanming; Fabregat, Antonio; Elser, Justin L; Weiser, Joel; Keays, Maria; Fuentes, Alfonso Munoz-Pomer; Petryszak, Robert; Stein, Lincoln D; Ware, Doreen; Jaiswal, Pankaj

2017-01-04

Plant Reactome (http://plantreactome.gramene.org/) is a free, open-source, curated plant pathway database portal, provided as part of the Gramene project. The database provides intuitive bioinformatics tools for the visualization, analysis and interpretation of pathway knowledge to support genome annotation, genome analysis, modeling, systems biology, basic research and education. Plant Reactome employs the structural framework of a plant cell to show metabolic, transport, genetic, developmental and signaling pathways. We manually curate molecular details of pathways in these domains for reference species Oryza sativa (rice) supported by published literature and annotation of well-characterized genes. Two hundred twenty-two rice pathways, 1025 reactions associated with 1173 proteins, 907 small molecules and 256 literature references have been curated to date. These reference annotations were used to project pathways for 62 model, crop and evolutionarily significant plant species based on gene homology. Database users can search and browse various components of the database, visualize curated baseline expression of pathway-associated genes provided by the Expression Atlas and upload and analyze their Omics datasets. The database also offers data access via Application Programming Interfaces (APIs) and in various standardized pathway formats, such as SBML and BioPAX. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

A Dual-Route Perspective on Brain Activation in Response to Visual Words: Evidence for a Length by Lexicality Interaction in the Visual Word Form Area (VWFA)

PubMed Central

Schurz, Matthias; Sturm, Denise; Richlan, Fabio; Kronbichler, Martin; Ladurner, Gunther; Wimmer, Heinz

2010-01-01

Based on our previous work, we expected the Visual Word Form Area (VWFA) in the left ventral visual pathway to be engaged by both whole-word recognition and by serial sublexical coding of letter strings. To examine this double function, a phonological lexical decision task (i.e., “Does xxx sound like an existing word?”) presented short and long letter strings of words, pseudohomophones, and pseudowords (e.g., Taxi, Taksi and Tazi). Main findings were that the length effect for words was limited to occipital regions and absent in the VWFA. In contrast, a marked length effect for pseudowords was found throughout the ventral visual pathway including the VWFA, as well as in regions presumably engaged by visual attention and silent-articulatory processes. The length by lexicality interaction on brain activation corresponds to well-established behavioral findings of a length by lexicality interaction on naming latencies and speaks for the engagement of the VWFA by both lexical and sublexical processes. PMID:19896538

A dual-route perspective on brain activation in response to visual words: evidence for a length by lexicality interaction in the visual word form area (VWFA).

PubMed

Schurz, Matthias; Sturm, Denise; Richlan, Fabio; Kronbichler, Martin; Ladurner, Gunther; Wimmer, Heinz

2010-02-01

Based on our previous work, we expected the Visual Word Form Area (VWFA) in the left ventral visual pathway to be engaged by both whole-word recognition and by serial sublexical coding of letter strings. To examine this double function, a phonological lexical decision task (i.e., "Does xxx sound like an existing word?") presented short and long letter strings of words, pseudohomophones, and pseudowords (e.g., Taxi, Taksi and Tazi). Main findings were that the length effect for words was limited to occipital regions and absent in the VWFA. In contrast, a marked length effect for pseudowords was found throughout the ventral visual pathway including the VWFA, as well as in regions presumably engaged by visual attention and silent-articulatory processes. The length by lexicality interaction on brain activation corresponds to well-established behavioral findings of a length by lexicality interaction on naming latencies and speaks for the engagement of the VWFA by both lexical and sublexical processes. Copyright (c) 2009 Elsevier Inc. All rights reserved.

Higher integrity of the motor and visual pathways in long-term video game players.

PubMed

Zhang, Yang; Du, Guijin; Yang, Yongxin; Qin, Wen; Li, Xiaodong; Zhang, Quan

2015-01-01

Long term video game players (VGPs) exhibit superior visual and motor skills compared with non-video game control subjects (NVGCs). However, the neural basis underlying the enhanced behavioral performance remains largely unknown. To clarify this issue, the present study compared the whiter matter integrity within the corticospinal tracts (CST), the superior longitudinal fasciculus (SLF), the inferior longitudinal fasciculus (ILF), and the inferior fronto-occipital fasciculus (IFOF) between the VGPs and the NVGCs using diffusion tensor imaging. Compared with the NVGCs, voxel-wise comparisons revealed significantly higher fractional anisotropy (FA) values in some regions within the left CST, left SLF, bilateral ILF, and IFOF in VGPs. Furthermore, higher FA values in the left CST at the level of cerebral peduncle predicted a faster response in visual attention tasks. These results suggest that higher white matter integrity in the motor and higher-tier visual pathways is associated with long-term video game playing, which may contribute to the understanding on how video game play influences motor and visual performance.

Higher integrity of the motor and visual pathways in long-term video game players

PubMed Central

Du, Guijin; Yang, Yongxin; Qin, Wen; Li, Xiaodong; Zhang, Quan

2015-01-01

Long term video game players (VGPs) exhibit superior visual and motor skills compared with non-video game control subjects (NVGCs). However, the neural basis underlying the enhanced behavioral performance remains largely unknown. To clarify this issue, the present study compared the whiter matter integrity within the corticospinal tracts (CST), the superior longitudinal fasciculus (SLF), the inferior longitudinal fasciculus (ILF), and the inferior fronto-occipital fasciculus (IFOF) between the VGPs and the NVGCs using diffusion tensor imaging. Compared with the NVGCs, voxel-wise comparisons revealed significantly higher fractional anisotropy (FA) values in some regions within the left CST, left SLF, bilateral ILF, and IFOF in VGPs. Furthermore, higher FA values in the left CST at the level of cerebral peduncle predicted a faster response in visual attention tasks. These results suggest that higher white matter integrity in the motor and higher-tier visual pathways is associated with long-term video game playing, which may contribute to the understanding on how video game play influences motor and visual performance. PMID:25805981

Assessing and Modulating Kynurenine Pathway Dynamics in Huntington's Disease: Focus on Kynurenine 3-Monooxygenase.

PubMed

Sathyasaikumar, Korrapati V; Breda, Carlo; Schwarcz, Robert; Giorgini, Flaviano

2018-01-01

The link between disturbances in kynurenine pathway (KP) metabolism and Huntington's disease (HD) pathogenesis has been explored for a number of years. Several novel genetic and pharmacological tools have recently been developed to modulate key regulatory steps in the KP such as the reaction catalyzed by the enzyme kynurenine 3-monooxygenase (KMO). This insight has offered new options for exploring the mechanistic link between this metabolic pathway and HD, and provided novel opportunities for the development of candidate drug-like compounds. Here, we present an overview of the field, focusing on some novel approaches for interrogating the pathway experimentally.

Gene expression analysis of colorectal cancer by bioinformatics strategy.

PubMed

Cui, Meng; Yuan, Junhua; Li, Jun; Sun, Bing; Li, Tao; Li, Yuantao; Wu, Guoliang

2014-10-01

We used bioinformatics technology to analyze gene expression profiles involved in colorectal cancer tissue samples and healthy controls. In this paper, we downloaded the gene expression profile GSE4107 from Gene Expression Omnibus (GEO) database, in which a total of 22 chips were available, including normal colonic mucosa tissue from normal healthy donors (n=10), colorectal cancer tissue samples from colorectal patients (n=33). To further understand the biological functions of the screened DGEs, the KEGG pathway enrichment analysis were conducted. Then we built a transcriptome network to study differentially co-expressed links. A total of 3151 DEGs of CRC were selected. Besides, total 164 DCGs (Differentially Coexpressed Gene, DCG) and 29279 DCLs (Differentially Co-expressed Link, DCL) were obtained. Furthermore, the significantly enriched KEGG pathways were Endocytosis, Calcium signaling pathway, Vascular smooth muscle contraction, Linoleic acid metabolism, Arginine and proline metabolism, Inositol phosphate metabolism and MAPK signaling pathway. Our results show that the generation of CRC involves multiple genes, TFs and pathways. Several signal and immune pathways are linked to CRC and give us more clues in the process of CRC. Hence, our work would pave ways for novel diagnosis of CRC, and provided theoretical guidance into cancer therapy.

Early-Stage Visual Processing and Cortical Amplification Deficits in Schizophrenia

PubMed Central

Butler, Pamela D.; Zemon, Vance; Schechter, Isaac; Saperstein, Alice M.; Hoptman, Matthew J.; Lim, Kelvin O.; Revheim, Nadine; Silipo, Gail; Javitt, Daniel C.

2005-01-01

Background Patients with schizophrenia show deficits in early-stage visual processing, potentially reflecting dysfunction of the magnocellular visual pathway. The magnocellular system operates normally in a nonlinear amplification mode mediated by glutamatergic (N-methyl-d-aspartate) receptors. Investigating magnocellular dysfunction in schizophrenia therefore permits evaluation of underlying etiologic hypotheses. Objectives To evaluate magnocellular dysfunction in schizophrenia, relative to known neurochemical and neuroanatomical substrates, and to examine relationships between electrophysiological and behavioral measures of visual pathway dysfunction and relationships with higher cognitive deficits. Design, Setting, and Participants Between-group study at an inpatient state psychiatric hospital and out-patient county psychiatric facilities. Thirty-three patients met DSM-IV criteria for schizophrenia or schizoaffective disorder, and 21 nonpsychiatric volunteers of similar ages composed the control group. Main Outcome Measures (1) Magnocellular and parvocellular evoked potentials, analyzed using nonlinear (Michaelis-Menten) and linear contrast gain approaches; (2) behavioral contrast sensitivity measures; (3) white matter integrity; (4) visual and nonvisual neuropsychological measures, and (5) clinical symptom and community functioning measures. Results Patients generated evoked potentials that were significantly reduced in response to magnocellular-biased, but not parvocellular-biased, stimuli (P=.001). Michaelis-Menten analyses demonstrated reduced contrast gain of the magnocellular system (P=.001). Patients showed decreased contrast sensitivity to magnocellular-biased stimuli (P<.001). Evoked potential deficits were significantly related to decreased white matter integrity in the optic radiations (P<.03). Evoked potential deficits predicted impaired contrast sensitivity (P=.002), which was in turn related to deficits in complex visual processing (P≤.04). Both evoked potential (P≤.04) and contrast sensitivity (P=.01) measures significantly predicted community functioning. Conclusions These findings confirm the existence of early-stage visual processing dysfunction in schizophrenia and provide the first evidence that such deficits are due to decreased nonlinear signal amplification, consistent with glutamatergic theories. Neuroimaging studies support the hypothesis of dysfunction within low-level visual pathways involving thalamocortical radiations. Deficits in early-stage visual processing significantly predict higher cognitive deficits. PMID:15867102

Evolution and Optimality of Similar Neural Mechanisms for Perception and Action during Search

PubMed Central

Zhang, Sheng; Eckstein, Miguel P.

2010-01-01

A prevailing theory proposes that the brain's two visual pathways, the ventral and dorsal, lead to differing visual processing and world representations for conscious perception than those for action. Others have claimed that perception and action share much of their visual processing. But which of these two neural architectures is favored by evolution? Successful visual search is life-critical and here we investigate the evolution and optimality of neural mechanisms mediating perception and eye movement actions for visual search in natural images. We implement an approximation to the ideal Bayesian searcher with two separate processing streams, one controlling the eye movements and the other stream determining the perceptual search decisions. We virtually evolved the neural mechanisms of the searchers' two separate pathways built from linear combinations of primary visual cortex receptive fields (V1) by making the simulated individuals' probability of survival depend on the perceptual accuracy finding targets in cluttered backgrounds. We find that for a variety of targets, backgrounds, and dependence of target detectability on retinal eccentricity, the mechanisms of the searchers' two processing streams converge to similar representations showing that mismatches in the mechanisms for perception and eye movements lead to suboptimal search. Three exceptions which resulted in partial or no convergence were a case of an organism for which the targets are equally detectable across the retina, an organism with sufficient time to foveate all possible target locations, and a strict two-pathway model with no interconnections and differential pre-filtering based on parvocellular and magnocellular lateral geniculate cell properties. Thus, similar neural mechanisms for perception and eye movement actions during search are optimal and should be expected from the effects of natural selection on an organism with limited time to search for food that is not equi-detectable across its retina and interconnected perception and action neural pathways. PMID:20838589

The Effect of Linked Learning Certified Pathways on Selected Student Outcomes

ERIC Educational Resources Information Center

Fitzgerald, Robert; Ottem, Randolph; Hufford, Justine

2016-01-01

This report examines outcomes for grade-12 students in academic years (AY) 2010-11, 2011-12, and 2012-13 who were enrolled in a Linked Learning certified pathway (LLCP) in California. Outcomes include student engagement in learning, measured by high school attendance and discipline events, as well as college readiness and postsecondary enrollment.…

Vocations: The Link between Post-Compulsory Education and the Labour Market. What the Research Says For... Industry

ERIC Educational Resources Information Center

Wheelahan, Leesa; Buchanan, John; Yu, Serena

2015-01-01

This summary brings together the relevant key findings for industry from the research program "Vocations: The Link between Post-Compulsory Education and the Labour Market." The program was comprised of three different strands: (1) pathways from VET in Schools, (2) pathways within and between vocational education and training (VET) and…

Late onset of a persistent, deep stromal scarring after PRK and corneal cross-linking in a patient with forme fruste keratoconus.

PubMed

Güell, Jose L; Verdaguer, Paula; Elies, Daniel; Gris, Oscar; Manero, Felicidad

2014-04-01

To present a case of a late, deep stromal scar in a 22-year-old patient with forme fruste keratoconus who underwent combined corneal cross-linking and photorefractive keratectomy (PRK). Topography-guided corneal cross-linking combined with corneal PRK (without complications) was performed in both eyes with a delay of 2 weeks between each eye. At the 5-month postoperative examination of the right eye, a localized corneal haze was circumscribed to the posterior deep stroma, signifying a decrease of visual acuity. However, this improved partially and temporarily when treated with topical corticoids during 2 years of follow-up and then reoccurred, affecting the corrected distance visual acuity. To the authors' knowledge, this is the first documented, clinical case presenting a deep stromal affectation without endothelial decompensation and visual acuity affectation as a postoperative complication following topography-guided PRK and corneal cross-linking. Copyright 2014, SLACK Incorporated.

Facilitated Protein Association via Engineered Target Search Pathways Visualized by Paramagnetic NMR Spectroscopy.

PubMed

An, So Young; Kim, Eun-Hee; Suh, Jeong-Yong

2018-06-05

Proteins assemble to form functional complexes via the progressive evolution of nonspecific complexes formed by transient encounters. This target search process generally involves multiple routes that lead the initial encounters to the final complex. In this study, we have employed NMR paramagnetic relaxation enhancement to visualize the encounter complexes between histidine-containing phosphocarrier protein and the N-terminal domain of enzyme I and demonstrate that protein association can be significantly enhanced by engineering on-pathways. Specifically, mutations in surface charges away from the binding interface can elicit new on-pathway encounter complexes, increasing their binding affinity by an order of magnitude. The structure of these encounter complexes indicates that such on-pathways extend the built-in target search process of the native protein complex. Furthermore, blocking on-pathways by countering mutations reverts their binding affinity. Our study thus illustrates that protein interactions can be engineered by rewiring the target search process. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

PubMed

Beltrame, Luca; Calura, Enrica; Popovici, Razvan R; Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

2011-08-01

Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and 'wet lab' scientists. The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X.

The direct, not V1-mediated, functional influence between the thalamus and middle temporal complex in the human brain is modulated by the speed of visual motion.

PubMed

Gaglianese, A; Costagli, M; Ueno, K; Ricciardi, E; Bernardi, G; Pietrini, P; Cheng, K

2015-01-22

The main visual pathway that conveys motion information to the middle temporal complex (hMT+) originates from the primary visual cortex (V1), which, in turn, receives spatial and temporal features of the perceived stimuli from the lateral geniculate nucleus (LGN). In addition, visual motion information reaches hMT+ directly from the thalamus, bypassing the V1, through a direct pathway. We aimed at elucidating whether this direct route between LGN and hMT+ represents a 'fast lane' reserved to high-speed motion, as proposed previously, or it is merely involved in processing motion information irrespective of speeds. We evaluated functional magnetic resonance imaging (fMRI) responses elicited by moving visual stimuli and applied connectivity analyses to investigate the effect of motion speed on the causal influence between LGN and hMT+, independent of V1, using the Conditional Granger Causality (CGC) in the presence of slow and fast visual stimuli. Our results showed that at least part of the visual motion information from LGN reaches hMT+, bypassing V1, in response to both slow and fast motion speeds of the perceived stimuli. We also investigated whether motion speeds have different effects on the connections between LGN and functional subdivisions within hMT+: direct connections between LGN and MT-proper carry mainly slow motion information, while connections between LGN and MST carry mainly fast motion information. The existence of a parallel pathway that connects the LGN directly to hMT+ in response to both slow and fast speeds may explain why MT and MST can still respond in the presence of V1 lesions. Copyright © 2014 IBRO. Published by Elsevier Ltd. All rights reserved.

Processing of single-photon responses in the mammalian On and Off retinal pathways at the sensitivity limit of vision

PubMed Central

2017-01-01

Visually guided behaviour at its sensitivity limit relies on single-photon responses originating in a small number of rod photoreceptors. For decades, researchers have debated the neural mechanisms and noise sources that underlie this striking sensitivity. To address this question, we need to understand the constraints arising from the retinal output signals provided by distinct retinal ganglion cell types. It has recently been shown in the primate retina that On and Off parasol ganglion cells, the cell types likely to underlie light detection at the absolute visual threshold, differ fundamentally not only in response polarity, but also in the way they handle single-photon responses originating in rods. The On pathway provides the brain with a thresholded, low-noise readout and the Off pathway with a noisy, linear readout. We outline the mechanistic basis of these different coding strategies and analyse their implications for detecting the weakest light signals. We show that high-fidelity, nonlinear signal processing in the On pathway comes with costs: more single-photon responses are lost and their propagation is delayed compared with the Off pathway. On the other hand, the responses of On ganglion cells allow better intensity discrimination compared with the Off ganglion cell responses near visual threshold. This article is part of the themed issue ‘Vision in dim light’. PMID:28193818

Processing of single-photon responses in the mammalian On and Off retinal pathways at the sensitivity limit of vision.

PubMed

Takeshita, Daisuke; Smeds, Lina; Ala-Laurila, Petri

2017-04-05

Visually guided behaviour at its sensitivity limit relies on single-photon responses originating in a small number of rod photoreceptors. For decades, researchers have debated the neural mechanisms and noise sources that underlie this striking sensitivity. To address this question, we need to understand the constraints arising from the retinal output signals provided by distinct retinal ganglion cell types. It has recently been shown in the primate retina that On and Off parasol ganglion cells, the cell types likely to underlie light detection at the absolute visual threshold, differ fundamentally not only in response polarity, but also in the way they handle single-photon responses originating in rods. The On pathway provides the brain with a thresholded, low-noise readout and the Off pathway with a noisy, linear readout. We outline the mechanistic basis of these different coding strategies and analyse their implications for detecting the weakest light signals. We show that high-fidelity, nonlinear signal processing in the On pathway comes with costs: more single-photon responses are lost and their propagation is delayed compared with the Off pathway. On the other hand, the responses of On ganglion cells allow better intensity discrimination compared with the Off ganglion cell responses near visual threshold.This article is part of the themed issue 'Vision in dim light'. © 2017 The Authors.

18F-FDOPA PET/CT or PET/MRI in Measuring Tumors in Patients With Newly-Diagnosed or Recurrent Gliomas

ClinicalTrials.gov

2017-01-30

Adult Anaplastic Ependymoma; Adult Anaplastic Oligodendroglioma; Adult Brain Stem Glioma; Adult Diffuse Astrocytoma; Adult Giant Cell Glioblastoma; Adult Glioblastoma; Adult Gliosarcoma; Adult Mixed Glioma; Adult Oligodendroglioma; Adult Pilocytic Astrocytoma; Adult Pineal Gland Astrocytoma; Adult Subependymal Giant Cell Astrocytoma; Childhood High-grade Cerebellar Astrocytoma; Childhood High-grade Cerebral Astrocytoma; Childhood Low-grade Cerebellar Astrocytoma; Childhood Low-grade Cerebral Astrocytoma; Recurrent Adult Brain Tumor; Recurrent Childhood Anaplastic Astrocytoma; Recurrent Childhood Anaplastic Oligoastrocytoma; Recurrent Childhood Anaplastic Oligodendroglioma; Recurrent Childhood Brain Stem Glioma; Recurrent Childhood Cerebellar Astrocytoma; Recurrent Childhood Cerebral Astrocytoma; Recurrent Childhood Diffuse Astrocytoma; Recurrent Childhood Fibrillary Astrocytoma; Recurrent Childhood Gemistocytic Astrocytoma; Recurrent Childhood Giant Cell Glioblastoma; Recurrent Childhood Glioblastoma; Recurrent Childhood Gliomatosis Cerebri; Recurrent Childhood Gliosarcoma; Recurrent Childhood Oligoastrocytoma; Recurrent Childhood Oligodendroglioma; Recurrent Childhood Pilomyxoid Astrocytoma; Recurrent Childhood Protoplasmic Astrocytoma; Recurrent Childhood Subependymal Giant Cell Astrocytoma; Recurrent Childhood Visual Pathway and Hypothalamic Glioma; Recurrent Childhood Visual Pathway Glioma; Untreated Childhood Anaplastic Astrocytoma; Untreated Childhood Anaplastic Oligoastrocytoma; Untreated Childhood Anaplastic Oligodendroglioma; Untreated Childhood Brain Stem Glioma; Untreated Childhood Cerebellar Astrocytoma; Untreated Childhood Cerebral Astrocytoma; Untreated Childhood Diffuse Astrocytoma; Untreated Childhood Fibrillary Astrocytoma; Untreated Childhood Gemistocytic Astrocytoma; Untreated Childhood Giant Cell Glioblastoma; Untreated Childhood Glioblastoma; Untreated Childhood Gliomatosis Cerebri; Untreated Childhood Gliosarcoma; Untreated Childhood Oligoastrocytoma; Untreated Childhood Oligodendroglioma; Untreated Childhood Pilomyxoid Astrocytoma; Untreated Childhood Protoplasmic Astrocytoma; Untreated Childhood Subependymal Giant Cell Astrocytoma; Untreated Childhood Visual Pathway and Hypothalamic Glioma; Untreated Childhood Visual Pathway Glioma

C-fos induction in forebrain areas of two different visual pathways during consolidation of sexual imprinting in the zebra finch (Taeniopygia guttata).

PubMed

Sadananda, Monika; Bischof, Hans-Joachim

2006-10-16

Two forebrain areas in the hyperpallium apicale and in the lateral nidopallium of isolated male zebra finches are highly active (2-deoxyglucose technique) on exposure to females for the first time, that is first courtship. These areas also demonstrate enhanced neuronal plasticity when screened with c-fos immunocytochemistry. Both are areas involved in the processing of visual information conveyed by the two major visual pathways in birds, strengthening our hypothesis that courtship in the zebra finch is a visually guided behaviour. First courtship and chased birds show enhanced c-fos induction in the hyperpallial area, which could represent neuronal activity reflecting changes in the immediate environment. The enhanced expression of fos in first courtship birds in lateral nidopallial neurons indicates imminent long-lasting changes at the synaptic level that form the substrate for imprinting, a stable form of learning in birds.

Dynamic Integration of Task-Relevant Visual Features in Posterior Parietal Cortex

PubMed Central

Freedman, David J.

2014-01-01

Summary The primate visual system consists of multiple hierarchically organized cortical areas, each specialized for processing distinct aspects of the visual scene. For example, color and form are encoded in ventral pathway areas such as V4 and inferior temporal cortex, while motion is preferentially processed in dorsal pathway areas such as the middle temporal area. Such representations often need to be integrated perceptually to solve tasks which depend on multiple features. We tested the hypothesis that the lateral intraparietal area (LIP) integrates disparate task-relevant visual features by recording from LIP neurons in monkeys trained to identify target stimuli composed of conjunctions of color and motion features. We show that LIP neurons exhibit integrative representations of both color and motion features when they are task relevant, and task-dependent shifts of both direction and color tuning. This suggests that LIP plays a role in flexibly integrating task-relevant sensory signals. PMID:25199703

Perceptual learning in visual search: fast, enduring, but non-specific.

PubMed

Sireteanu, R; Rettenbach, R

1995-07-01

Visual search has been suggested as a tool for isolating visual primitives. Elementary "features" were proposed to involve parallel search, while serial search is necessary for items without a "feature" status, or, in some cases, for conjunctions of "features". In this study, we investigated the role of practice in visual search tasks. We found that, under some circumstances, initially serial tasks can become parallel after a few hundred trials. Learning in visual search is far less specific than learning of visual discriminations and hyperacuity, suggesting that it takes place at another level in the central visual pathway, involving different neural circuits.

A novel p.Gly603Arg mutation in CACNA1F causes Åland island eye disease and incomplete congenital stationary night blindness phenotypes in a family

PubMed Central

Vincent, Ajoy; Wright, Tom; Day, Megan A.; Westall, Carol A.

2011-01-01

Purpose To report, for the first time, that X-linked incomplete congenital stationary night blindness (CSNB2A) and Åland island eye disease (AIED) phenotypes coexist in a molecularly confirmed pedigree and to present novel phenotypic characteristics of calcium channel alpha-1F subunit gene (CACNA1F)-related disease. Methods Two affected subjects (the proband and his maternal grandfather) and an unaffected obligate carrier (the proband’s mother) underwent detailed ophthalmological evaluation, fundus autofluorescence imaging, and spectral-domain optical coherence tomography. Goldmann visual field assessment and full-field electroretinogram (ERG) were performed in the two affected subjects, and multichannel flash visual evoked potential was performed on the proband. Scotopic 15 Hz flicker ERG series were performed in both affected subjects to evaluate the function of the slow and fast rod pathways. Haplotype analysis using polymorphic microsatellite markers flanking CACNA1F was performed in all three family members. The proband’s DNA was sequenced for mutations in the coding sequence of CACNA1F and nyctalopin (NYX) genes. Segregation analysis was performed in the family. Results Both affected subjects had symptoms of nonprogressive nyctalopia since childhood, while the proband also had photophobia. Both cases had a distance visual acuity of 20/50 or better in each eye, normal contrast sensitivity, and an incomplete type of Schubert-Bornschein ERGs. The proband also had high myopia, a mild red-green color deficit, hypopigmented fundus, and foveal hypoplasia with no evidence of chiasmal misrouting. Spectral-domain optical coherence tomography confirmed the presence of foveal hypoplasia in the proband. The clinical phenotype of the proband and his maternal grandfather fit the clinical description of AIED and CSNB2A, respectively. The fundus autofluorescence and the visual fields were normal in both cases; the scotopic 15 Hz flicker ERG demonstrated only fast rod pathway activity in both. Both affected cases shared the same haplotype across CACNA1F. The proband carried a novel hemizygous c.1807G>C mutation (p.G603R) in the CACNA1F gene. The change segregated with the disease phenotypes and was not identified in 360 control chromosomes. No mutations were identified in NYX. Conclusions This report of a missense mutation in CACNA1F causing AIED and CSNB2A phenotypes in a family confirms that both diseases are allelic and that other genetic or environmental modifiers influence the expression of CACNA1F. This is the first report to suggest that in CACNA1F-related disease, the rod system activity is predominantly from the fast rod pathways. PMID:22194652

The neural subjective frame: from bodily signals to perceptual consciousness

PubMed Central

Park, Hyeong-Dong; Tallon-Baudry, Catherine

2014-01-01

The report ‘I saw the stimulus’ operationally defines visual consciousness, but where does the ‘I’ come from? To account for the subjective dimension of perceptual experience, we introduce the concept of the neural subjective frame. The neural subjective frame would be based on the constantly updated neural maps of the internal state of the body and constitute a neural referential from which first person experience can be created. We propose to root the neural subjective frame in the neural representation of visceral information which is transmitted through multiple anatomical pathways to a number of target sites, including posterior insula, ventral anterior cingulate cortex, amygdala and somatosensory cortex. We review existing experimental evidence showing that the processing of external stimuli can interact with visceral function. The neural subjective frame is a low-level building block of subjective experience which is not explicitly experienced by itself which is necessary but not sufficient for perceptual experience. It could also underlie other types of subjective experiences such as self-consciousness and emotional feelings. Because the neural subjective frame is tightly linked to homeostatic regulations involved in vigilance, it could also make a link between state and content consciousness. PMID:24639580

The neural subjective frame: from bodily signals to perceptual consciousness.

PubMed

Park, Hyeong-Dong; Tallon-Baudry, Catherine

2014-05-05

The report 'I saw the stimulus' operationally defines visual consciousness, but where does the 'I' come from? To account for the subjective dimension of perceptual experience, we introduce the concept of the neural subjective frame. The neural subjective frame would be based on the constantly updated neural maps of the internal state of the body and constitute a neural referential from which first person experience can be created. We propose to root the neural subjective frame in the neural representation of visceral information which is transmitted through multiple anatomical pathways to a number of target sites, including posterior insula, ventral anterior cingulate cortex, amygdala and somatosensory cortex. We review existing experimental evidence showing that the processing of external stimuli can interact with visceral function. The neural subjective frame is a low-level building block of subjective experience which is not explicitly experienced by itself which is necessary but not sufficient for perceptual experience. It could also underlie other types of subjective experiences such as self-consciousness and emotional feelings. Because the neural subjective frame is tightly linked to homeostatic regulations involved in vigilance, it could also make a link between state and content consciousness.

CellLineNavigator: a workbench for cancer cell line analysis

PubMed Central

Krupp, Markus; Itzel, Timo; Maass, Thorsten; Hildebrandt, Andreas; Galle, Peter R.; Teufel, Andreas

2013-01-01

The CellLineNavigator database, freely available at http://www.medicalgenomics.org/celllinenavigator, is a web-based workbench for large scale comparisons of a large collection of diverse cell lines. It aims to support experimental design in the fields of genomics, systems biology and translational biomedical research. Currently, this compendium holds genome wide expression profiles of 317 different cancer cell lines, categorized into 57 different pathological states and 28 individual tissues. To enlarge the scope of CellLineNavigator, the database was furthermore closely linked to commonly used bioinformatics databases and knowledge repositories. To ensure easy data access and search ability, a simple data and an intuitive querying interface were implemented. It allows the user to explore and filter gene expression, focusing on pathological or physiological conditions. For a more complex search, the advanced query interface may be used to query for (i) differentially expressed genes; (ii) pathological or physiological conditions; or (iii) gene names or functional attributes, such as Kyoto Encyclopaedia of Genes and Genomes pathway maps. These queries may also be combined. Finally, CellLineNavigator allows additional advanced analysis of differentially regulated genes by a direct link to the Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resources. PMID:23118487

Blindness alters the microstructure of the ventral but not the dorsal visual stream.

PubMed

Reislev, Nina L; Kupers, Ron; Siebner, Hartwig R; Ptito, Maurice; Dyrby, Tim B

2016-07-01

Visual deprivation from birth leads to reorganisation of the brain through cross-modal plasticity. Although there is a general agreement that the primary afferent visual pathways are altered in congenitally blind individuals, our knowledge about microstructural changes within the higher-order visual streams, and how this is affected by onset of blindness, remains scant. We used diffusion tensor imaging and tractography to investigate microstructural features in the dorsal (superior longitudinal fasciculus) and ventral (inferior longitudinal and inferior fronto-occipital fasciculi) visual pathways in 12 congenitally blind, 15 late blind and 15 normal sighted controls. We also studied six prematurely born individuals with normal vision to control for the effects of prematurity on brain connectivity. Our data revealed a reduction in fractional anisotropy in the ventral but not the dorsal visual stream for both congenitally and late blind individuals. Prematurely born individuals, with normal vision, did not differ from normal sighted controls, born at term. Our data suggest that although the visual streams are structurally developing without normal visual input from the eyes, blindness selectively affects the microstructure of the ventral visual stream regardless of the time of onset. We suggest that the decreased fractional anisotropy of the ventral stream in the two groups of blind subjects is the combined result of both degenerative and cross-modal compensatory processes, affecting normal white matter development.

Distribution and specificity of S-cone ("blue cone") signals in subcortical visual pathways.

PubMed

Martin, Paul R; Lee, Barry B

2014-03-01

We review here the distribution of S-cone signals and properties of S-cone recipient receptive fields in subcortical pathways. Nearly everything we know about S-cone signals in the subcortical visual system comes from the study of visual systems in cats and primates (monkeys); in this review, we concentrate on results from macaque and marmoset monkeys. We discuss segregation of S-cone recipient (blue-on and blue-off) receptive fields in the dorsal lateral geniculate nucleus and describe their receptive field properties. We treat in some detail the question of detecting weak S-cone signals as an introduction for newcomers to the field. Finally, we briefly consider the question on how S-cone signals are distributed among nongeniculate targets.

Graphite Web: web tool for gene set analysis exploiting pathway topology

PubMed Central

Sales, Gabriele; Calura, Enrica; Martini, Paolo; Romualdi, Chiara

2013-01-01

Graphite web is a novel web tool for pathway analyses and network visualization for gene expression data of both microarray and RNA-seq experiments. Several pathway analyses have been proposed either in the univariate or in the global and multivariate context to tackle the complexity and the interpretation of expression results. These methods can be further divided into ‘topological’ and ‘non-topological’ methods according to their ability to gain power from pathway topology. Biological pathways are, in fact, not only gene lists but can be represented through a network where genes and connections are, respectively, nodes and edges. To this day, the most used approaches are non-topological and univariate although they miss the relationship among genes. On the contrary, topological and multivariate approaches are more powerful, but difficult to be used by researchers without bioinformatic skills. Here we present Graphite web, the first public web server for pathway analysis on gene expression data that combines topological and multivariate pathway analyses with an efficient system of interactive network visualizations for easy results interpretation. Specifically, Graphite web implements five different gene set analyses on three model organisms and two pathway databases. Graphite Web is freely available at http://graphiteweb.bio.unipd.it/. PMID:23666626

Probing the substrate specificity of Golgi alpha-mannosidase II by use of synthetic oligosaccharides and a catalytic nucleophile mutant.

PubMed

Zhong, Wei; Kuntz, Douglas A; Ember, Brian; Singh, Harminder; Moremen, Kelley W; Rose, David R; Boons, Geert-Jan

2008-07-16

Inhibition of Golgi alpha-mannosidase II (GMII), which acts late in the N-glycan processing pathway, provides a route to blocking cancer-induced changes in cell surface oligosaccharide structures. To probe the substrate requirements of GMII, oligosaccharides were synthesized that contained an alpha(1,3)- or alpha(1,6)-linked 1-thiomannoside. Surprisingly, these oligosaccharides were not observed in X-ray crystal structures of native Drosophila GMII (dGMII). However, a mutant enzyme in which the catalytic nucleophilic aspartate was changed to alanine (D204A) allowed visualization of soaked oligosaccharides and led to the identification of the binding site for the alpha(1,3)-linked mannoside of the natural substrate. These studies also indicate that the conformational change of the bound mannoside to a high-energy B 2,5 conformation is facilitated by steric hindrance from, and the formation of strong hydrogen bonds to, Asp204. The observation that 1-thio-linked mannosides are not well tolerated by the catalytic site of dGMII led to the synthesis of a pentasaccharide containing the alpha(1,6)-linked Man of the natural substrate and the beta(1,2)-linked GlcNAc moiety proposed to be accommodated by the extended binding site of the enzyme. A cocrystal structure of this compound with the D204A enzyme revealed the molecular interactions with the beta(1,2)-linked GlcNAc. The structure is consistent with the approximately 80-fold preference of dGMII for the cleavage of substrates containing a nonreducing beta(1,2)-linked GlcNAc. By contrast, the lysosomal mannosidase lacks an equivalent GlcNAc binding site and kinetic analysis indicates oligomannoside substrates without non-reducing-terminal GlcNAc modifications are preferred, suggesting that selective inhibitors for GMII could exploit the additional binding specificity of the GlcNAc binding site.

The anti-apoptotic activity associated with phosphatidylinositol transfer protein alpha activates the MAPK and Akt/PKB pathway.

PubMed

Schenning, Martijn; Goedhart, Joachim; Gadella, Theodorus W J; Avram, Diana; Wirtz, Karel W A; Snoek, Gerry T

2008-10-01

The conditioned medium (CM) from mouse NIH3T3 fibroblast cells overexpressing phosphatidylinositol transfer protein alpha (PI-TPalpha; SPIalpha cells) demonstrates an increased anti-apoptotic activity compared with CM from wild type NIH3T3 (wtNIH3T3) cells. As previously shown, the anti-apoptotic activity acts by activating a G protein-coupled receptor, most probably a cannabinoid 1 (CB1)-like receptor as the activity was blocked by both pertussis toxin and rimonabant [M. Schenning, C.M. van Tiel, D. Van Manen, J.C. Stam, B.M. Gadella, K.W. Wirtz and G.T. Snoek, Phosphatidylinositol transfer protein alpha regulates growth and apoptosis of NIH3T3 cells: involvement of a cannabinoid 1-like receptor, J. Lipid Res. 45 (2004) 1555-1564]. The CB1 receptor appears to be expressed in mouse fibroblast cells, at levels in the order SPIalpha>wtNIH3T3>SPIbeta cells (i.e. wild type cells overexpressing PI-TPbeta). Upon incubation of SPIbeta cells with the PI-TPalpha-dependent anti-apoptotic factors, both the ERK/MAP kinase and the Akt/PKB pathway are activated in a CB1 receptor dependent manner as shown by Western blotting. In addition, activation of ERK2 was also shown by EYFP-ERK2 translocation to the nucleus, as visualized by confocal laser scanning microscopy. The subsequent activation of the anti-apoptotic transcription factor NF-kappaB is in line with the increased resistance towards UV-induced apoptosis. On the other hand, receptor activation by CM from SPIalpha cells was not linked to phospholipase C activation as the YFP-labelled C2-domain of protein kinase C was not translocated to the plasma membrane of SPIbeta cells as visualized by confocal laser scanning microscopy.

Abnormal late visual responses and alpha oscillations in neurofibromatosis type 1: a link to visual and attention deficits

PubMed Central

2014-01-01

Background Neurofibromatosis type 1 (NF1) affects several areas of cognitive function including visual processing and attention. We investigated the neural mechanisms underlying the visual deficits of children and adolescents with NF1 by studying visual evoked potentials (VEPs) and brain oscillations during visual stimulation and rest periods. Methods Electroencephalogram/event-related potential (EEG/ERP) responses were measured during visual processing (NF1 n = 17; controls n = 19) and idle periods with eyes closed and eyes open (NF1 n = 12; controls n = 14). Visual stimulation was chosen to bias activation of the three detection mechanisms: achromatic, red-green and blue-yellow. Results We found significant differences between the groups for late chromatic VEPs and a specific enhancement in the amplitude of the parieto-occipital alpha amplitude both during visual stimulation and idle periods. Alpha modulation and the negative influence of alpha oscillations in visual performance were found in both groups. Conclusions Our findings suggest abnormal later stages of visual processing and enhanced amplitude of alpha oscillations supporting the existence of deficits in basic sensory processing in NF1. Given the link between alpha oscillations, visual perception and attention, these results indicate a neural mechanism that might underlie the visual sensitivity deficits and increased lapses of attention observed in individuals with NF1. PMID:24559228

Anorexia nervosa and body dysmorphic disorder are associated with abnormalities in processing visual information.

PubMed

Li, W; Lai, T M; Bohon, C; Loo, S K; McCurdy, D; Strober, M; Bookheimer, S; Feusner, J

2015-07-01

Anorexia nervosa (AN) and body dysmorphic disorder (BDD) are characterized by distorted body image and are frequently co-morbid with each other, although their relationship remains little studied. While there is evidence of abnormalities in visual and visuospatial processing in both disorders, no study has directly compared the two. We used two complementary modalities--event-related potentials (ERPs) and functional magnetic resonance imaging (fMRI)--to test for abnormal activity associated with early visual signaling. We acquired fMRI and ERP data in separate sessions from 15 unmedicated individuals in each of three groups (weight-restored AN, BDD, and healthy controls) while they viewed images of faces and houses of different spatial frequencies. We used joint independent component analyses to compare activity in visual systems. AN and BDD groups demonstrated similar hypoactivity in early secondary visual processing regions and the dorsal visual stream when viewing low spatial frequency faces, linked to the N170 component, as well as in early secondary visual processing regions when viewing low spatial frequency houses, linked to the P100 component. Additionally, the BDD group exhibited hyperactivity in fusiform cortex when viewing high spatial frequency houses, linked to the N170 component. Greater activity in this component was associated with lower attractiveness ratings of faces. Results provide preliminary evidence of similar abnormal spatiotemporal activation in AN and BDD for configural/holistic information for appearance- and non-appearance-related stimuli. This suggests a common phenotype of abnormal early visual system functioning, which may contribute to perceptual distortions.

Multidimensional structured data visualization method and apparatus, text visualization method and apparatus, method and apparatus for visualizing and graphically navigating the world wide web, method and apparatus for visualizing hierarchies

DOEpatents

Risch, John S [Kennewick, WA; Dowson, Scott T [West Richland, WA; Hart, Michelle L [Richland, WA; Hatley, Wes L [Kennewick, WA

2008-05-13

A method of displaying correlations among information objects comprises receiving a query against a database; obtaining a query result set; and generating a visualization representing the components of the result set, the visualization including one of a plane and line to represent a data field, nodes representing data values, and links showing correlations among fields and values. Other visualization methods and apparatus are disclosed.

Multidimensional structured data visualization method and apparatus, text visualization method and apparatus, method and apparatus for visualizing and graphically navigating the world wide web, method and apparatus for visualizing hierarchies

DOEpatents

Risch, John S [Kennewick, WA; Dowson, Scott T [West Richland, WA

2012-03-06

A method of displaying correlations among information objects includes receiving a query against a database; obtaining a query result set; and generating a visualization representing the components of the result set, the visualization including one of a plane and line to represent a data field, nodes representing data values, and links showing correlations among fields and values. Other visualization methods and apparatus are disclosed.

Vocations: The Link between Post-Compulsory Education and the Labour Market. What the Research Says For... Tertiary Education Providers & School Educators

ERIC Educational Resources Information Center

Wheelahan, Leesa; Buchanan, John; Yu, Serena

2015-01-01

This summary brings together the relevant key findings for tertiary education providers and school educators from the research program "Vocations: The Link between Post-Compulsory Education and the Labour Market." The program was comprised of three different strands: (1) pathways from VET in Schools, (2) pathways within and between…

Vocations: The Link between Post-Compulsory Education and the Labour Market. What the Research Says For... Qualification & Approval Bodies

ERIC Educational Resources Information Center

Wheelahan, Leesa; Buchanan, John; Yu, Serena

2015-01-01

This summary pulls together the relevant key findings for qualification and approval bodies from the research program "Vocations: The Link between Post-Compulsory Education and the Labour Market." The program was comprised of three different strands: (1) pathways from VET in Schools, (2) pathways within and between vocational education…

Vocations: The Link between Post-Compulsory Education and the Labour Market. What the Research Says For... Government & Policy-Makers

ERIC Educational Resources Information Center

Wheelahan, Leesa; Buchanan, John; Yu, Serena

2015-01-01

This summary brings together the relevant key findings for government and policy-makers from the research program "Vocations: The Link between Post-Compulsory Education and the Labour Market." The program was comprised of three different strands: (1) pathways from VET in Schools, (2) pathways within and between vocational education and…

Neurology of Learning Disabilities: What Will the Future Bring? The Answer Comes from the Successes of the Recent Past

ERIC Educational Resources Information Center

Galaburda, Albert M.

2005-01-01

Dyslexia may represent the first example of a LD whereby a possible pathway may link the observed behavior to an underlying neurological substrate that has a neurodevelopmental history beginning with an abnormal gene. Similar efforts are being made to link other cognitive disorders of development to a molecular pathway involved in brain…

The cost of making an eye movement: A direct link between visual working memory and saccade execution.

PubMed

Schut, Martijn J; Van der Stoep, Nathan; Postma, Albert; Van der Stigchel, Stefan

2017-06-01

To facilitate visual continuity across eye movements, the visual system must presaccadically acquire information about the future foveal image. Previous studies have indicated that visual working memory (VWM) affects saccade execution. However, the reverse relation, the effect of saccade execution on VWM load is less clear. To investigate the causal link between saccade execution and VWM, we combined a VWM task and a saccade task. Participants were instructed to remember one, two, or three shapes and performed either a No Saccade-, a Single Saccade- or a Dual (corrective) Saccade-task. The results indicate that items stored in VWM are reported less accurately if a single saccade-or a dual saccade-task is performed next to retaining items in VWM. Importantly, the loss of response accuracy for items retained in VWM by performing a saccade was similar to committing an extra item to VWM. In a second experiment, we observed no cost of executing a saccade for auditory working memory performance, indicating that executing a saccade exclusively taxes the VWM system. Our results suggest that the visual system presaccadically stores the upcoming retinal image, which has a similar VWM load as committing one extra item to memory and interferes with stored VWM content. After the saccade, the visual system can retrieve this item from VWM to evaluate saccade accuracy. Our results support the idea that VWM is a system which is directly linked to saccade execution and promotes visual continuity across saccades.

The Role of Visual Thinking in Writing the News Story

ERIC Educational Resources Information Center

Choo, Suzanne

2010-01-01

In this article, the author begins with a proposition asking what if visual thinking were privileged in the English classroom and then proceeds to elaborate on a curriculum grounded on three principles: (1) sense and perception as starting points; (2) meta-conceptual links between visual and verbal texts; and (3) the art of visualization in…

Visual Search Deficits Are Independent of Magnocellular Deficits in Dyslexia

ERIC Educational Resources Information Center

Wright, Craig M.; Conlon, Elizabeth G.; Dyck, Murray

2012-01-01

The aim of this study was to investigate the theory that visual magnocellular deficits seen in groups with dyslexia are linked to reading via the mechanisms of visual attention. Visual attention was measured with a serial search task and magnocellular function with a coherent motion task. A large group of children with dyslexia (n = 70) had slower…

Topographic organization, number, and laminar distribution of callosal cells connecting visual cortical areas 17 and 18 of normally pigmented and Siamese cats.

PubMed

Berman, N E; Grant, S

1992-07-01

The callosal connections between visual cortical areas 17 and 18 in adult normally pigmented and "Boston" Siamese cats were studied using degeneration methods, and by transport of WGA-HRP combined with electrophysiological mapping. In normal cats, over 90% of callosal neurons were located in the supragranular layers. The supragranular callosal cell zone spanned the area 17/18 border and extended, on average, some 2-3 mm into both areas to occupy a territory which was roughly co-extensive with the distribution of callosal terminations in these areas. The region of the visual field adjoining the vertical meridian that was represented by neurons in the supragranular callosal cell zone was shown to increase systematically with decreasing visual elevation. Thus, close to the area centralis, receptive-field centers recorded from within this zone extended only up to 5 deg into the contralateral hemifield but at elevations of -10 deg and -40 deg they extended as far as 8 deg and 14 deg, respectively, into this hemifield. This suggests an element of visual non-correspondence in the callosal pathway between these cortical areas, which may be an essential substrate for "coarse" stereopsis at the visual midline. In the Siamese cats, the callosal cell and termination zones in areas 17 and 18 were expanded in width compared to the normal animals, but the major components were less robust. The area 17/18 border was often devoid of callosal axons and, in particular, the number of supragranular layer neurons participating in the pathway were drastically reduced, to only about 25% of those found in the normally pigmented adults. The callosal zones contained representations of the contralateral and ipsilateral hemifields that were roughly mirror-symmetric about the vertical meridian, and both hemifield representations increased with decreasing visual elevation. The extent and severity of the anomalies observed were similar across individual cats, regardless of whether a strabismus was also present. The callosal pathway between these visual cortical areas in the Siamese cat has been considered "silent," since nearly all neurons within its territory are activated only by the contralateral eye. The paucity of supragranular pyramidal neurons involved in the pathway may explain this silence.

Design and Development of a Linked Open Data-Based Health Information Representation and Visualization System: Potentials and Preliminary Evaluation

PubMed Central

Kauppinen, Tomi; Keßler, Carsten; Fritz, Fleur

2014-01-01

Background Healthcare organizations around the world are challenged by pressures to reduce cost, improve coordination and outcome, and provide more with less. This requires effective planning and evidence-based practice by generating important information from available data. Thus, flexible and user-friendly ways to represent, query, and visualize health data becomes increasingly important. International organizations such as the World Health Organization (WHO) regularly publish vital data on priority health topics that can be utilized for public health policy and health service development. However, the data in most portals is displayed in either Excel or PDF formats, which makes information discovery and reuse difficult. Linked Open Data (LOD)—a new Semantic Web set of best practice of standards to publish and link heterogeneous data—can be applied to the representation and management of public level health data to alleviate such challenges. However, the technologies behind building LOD systems and their effectiveness for health data are yet to be assessed. Objective The objective of this study is to evaluate whether Linked Data technologies are potential options for health information representation, visualization, and retrieval systems development and to identify the available tools and methodologies to build Linked Data-based health information systems. Methods We used the Resource Description Framework (RDF) for data representation, Fuseki triple store for data storage, and Sgvizler for information visualization. Additionally, we integrated SPARQL query interface for interacting with the data. We primarily use the WHO health observatory dataset to test the system. All the data were represented using RDF and interlinked with other related datasets on the Web of Data using Silk—a link discovery framework for Web of Data. A preliminary usability assessment was conducted following the System Usability Scale (SUS) method. Results We developed an LOD-based health information representation, querying, and visualization system by using Linked Data tools. We imported more than 20,000 HIV-related data elements on mortality, prevalence, incidence, and related variables, which are freely available from the WHO global health observatory database. Additionally, we automatically linked 5312 data elements from DBpedia, Bio2RDF, and LinkedCT using the Silk framework. The system users can retrieve and visualize health information according to their interests. For users who are not familiar with SPARQL queries, we integrated a Linked Data search engine interface to search and browse the data. We used the system to represent and store the data, facilitating flexible queries and different kinds of visualizations. The preliminary user evaluation score by public health data managers and users was 82 on the SUS usability measurement scale. The need to write queries in the interface was the main reported difficulty of LOD-based systems to the end user. Conclusions The system introduced in this article shows that current LOD technologies are a promising alternative to represent heterogeneous health data in a flexible and reusable manner so that they can serve intelligent queries, and ultimately support decision-making. However, the development of advanced text-based search engines is necessary to increase its usability especially for nontechnical users. Further research with large datasets is recommended in the future to unfold the potential of Linked Data and Semantic Web for future health information systems development. PMID:25601195

Design and development of a linked open data-based health information representation and visualization system: potentials and preliminary evaluation.

PubMed

Tilahun, Binyam; Kauppinen, Tomi; Keßler, Carsten; Fritz, Fleur

2014-10-25

Healthcare organizations around the world are challenged by pressures to reduce cost, improve coordination and outcome, and provide more with less. This requires effective planning and evidence-based practice by generating important information from available data. Thus, flexible and user-friendly ways to represent, query, and visualize health data becomes increasingly important. International organizations such as the World Health Organization (WHO) regularly publish vital data on priority health topics that can be utilized for public health policy and health service development. However, the data in most portals is displayed in either Excel or PDF formats, which makes information discovery and reuse difficult. Linked Open Data (LOD)-a new Semantic Web set of best practice of standards to publish and link heterogeneous data-can be applied to the representation and management of public level health data to alleviate such challenges. However, the technologies behind building LOD systems and their effectiveness for health data are yet to be assessed. The objective of this study is to evaluate whether Linked Data technologies are potential options for health information representation, visualization, and retrieval systems development and to identify the available tools and methodologies to build Linked Data-based health information systems. We used the Resource Description Framework (RDF) for data representation, Fuseki triple store for data storage, and Sgvizler for information visualization. Additionally, we integrated SPARQL query interface for interacting with the data. We primarily use the WHO health observatory dataset to test the system. All the data were represented using RDF and interlinked with other related datasets on the Web of Data using Silk-a link discovery framework for Web of Data. A preliminary usability assessment was conducted following the System Usability Scale (SUS) method. We developed an LOD-based health information representation, querying, and visualization system by using Linked Data tools. We imported more than 20,000 HIV-related data elements on mortality, prevalence, incidence, and related variables, which are freely available from the WHO global health observatory database. Additionally, we automatically linked 5312 data elements from DBpedia, Bio2RDF, and LinkedCT using the Silk framework. The system users can retrieve and visualize health information according to their interests. For users who are not familiar with SPARQL queries, we integrated a Linked Data search engine interface to search and browse the data. We used the system to represent and store the data, facilitating flexible queries and different kinds of visualizations. The preliminary user evaluation score by public health data managers and users was 82 on the SUS usability measurement scale. The need to write queries in the interface was the main reported difficulty of LOD-based systems to the end user. The system introduced in this article shows that current LOD technologies are a promising alternative to represent heterogeneous health data in a flexible and reusable manner so that they can serve intelligent queries, and ultimately support decision-making. However, the development of advanced text-based search engines is necessary to increase its usability especially for nontechnical users. Further research with large datasets is recommended in the future to unfold the potential of Linked Data and Semantic Web for future health information systems development.

Neural networks for Braille reading by the blind.

PubMed

Sadato, N; Pascual-Leone, A; Grafman, J; Deiber, M P; Ibañez, V; Hallett, M

1998-07-01

To explore the neural networks used for Braille reading, we measured regional cerebral blood flow with PET during tactile tasks performed both by Braille readers blinded early in life and by sighted subjects. Eight proficient Braille readers were studied during Braille reading with both right and left index fingers. Eight-character, non-contracted Braille-letter strings were used, and subjects were asked to discriminate between words and non-words. To compare the behaviour of the brain of the blind and the sighted directly, non-Braille tactile tasks were performed by six different blind subjects and 10 sighted control subjects using the right index finger. The tasks included a non-discrimination task and three discrimination tasks (angle, width and character). Irrespective of reading finger (right or left), Braille reading by the blind activated the inferior parietal lobule, primary visual cortex, superior occipital gyri, fusiform gyri, ventral premotor area, superior parietal lobule, cerebellum and primary sensorimotor area bilaterally, also the right dorsal premotor cortex, right middle occipital gyrus and right prefrontal area. During non-Braille discrimination tasks, in blind subjects, the ventral occipital regions, including the primary visual cortex and fusiform gyri bilaterally were activated while the secondary somatosensory area was deactivated. The reverse pattern was found in sighted subjects where the secondary somatosensory area was activated while the ventral occipital regions were suppressed. These findings suggest that the tactile processing pathways usually linked in the secondary somatosensory area are rerouted in blind subjects to the ventral occipital cortical regions originally reserved for visual shape discrimination.

Certification Criteria for Linked Learning Pathways

ERIC Educational Resources Information Center

ConnectEd: The California Center for College and Career, 2010

2010-01-01

Pathways offer a promising strategy for transforming high schools and improving student outcomes. However, to achieve these desired results, pathways must be of high quality. To guide sites in planning and implementing such pathways, a design team of experts developed the criteria outlined in this document. Sites can choose to go through a…

Differentiating pathway-specific from nonspecific effects in high-throughput toxicity data: A foundation for prioritizing adverse outcome pathway development

EPA Science Inventory

The U.S. Environmental Protection Agency’s ToxCast program has screened thousands of chemicals for biological activity, primarily using high-throughput in vitro bioassays. Adverse outcome pathways (AOPs) offer a means to link pathway-specific biological activities with potential ...

Dyslexia Linked to Visual Strengths Useful in Astronomy

NASA Astrophysics Data System (ADS)

Schneps, Matthew H.; Brockmole, J. R.; Rose, L. T.; Pomplun, M.; Sonnert, G.; Greenhill, L. J.

2011-05-01

Dyslexia is a hereditary neurological condition characterized by difficulties in reading, writing, and spelling. The fact that those with dyslexia include many accomplished scientists, including some recognized with a Nobel Prize, has prompted researchers to suggest that the neurology of dyslexia may predispose these individuals to advantages in visually-intensive domains such as science. Here, we report evidence of a link between dyslexia and abilities for visual processing useful in astronomy. First, we show that when images of natural scenes are Gaussian-blurred, so as to remove high-frequency detail (and resemble many astronomical images), college students with dyslexia significantly outperform those who are typical readers in learning the spatial contexts presented. Second, we show that when the threshold ability to detect radio signatures characteristic of black holes is measured in a laboratory simulation, astrophysicists with dyslexia significantly outperform those who are typical readers in this task when the visual periphery is important. In a third experiment, using eye-tracking technologies, we demonstrate that visual strategies significantly correlate with success in the black hole task, but that college students with dyslexia tend not to employ the strategies most likely to lead to success. Collectively, these studies suggest that dyslexia is linked to neurological advantages useful in astronomical careers, but that left to their own devices students with dyslexia may not benefit from these advantages without practice or training. These studies imply that many students who are struggling to read may find successful careers in astronomy or other fields that build on visual advantages linked to their reading disability, but that education and training may be vital in helping these students realize their strengths. This material is based upon work supported by the George E. Burch Fellowship (Smithsonian Institution) and the National Science Foundation under Grants HRD-0726032 and HRD-0930962.

Collecting and Storing Blood and Brain Tumor Tissue Samples From Children With Brain Tumors

ClinicalTrials.gov

2017-12-11

Childhood Atypical Teratoid/Rhabdoid Tumor; Childhood Central Nervous System Germ Cell Tumor; Childhood Choroid Plexus Tumor; Childhood Craniopharyngioma; Childhood Grade I Meningioma; Childhood Grade II Meningioma; Childhood Grade III Meningioma; Childhood High-grade Cerebral Astrocytoma; Childhood Infratentorial Ependymoma; Childhood Low-grade Cerebral Astrocytoma; Childhood Oligodendroglioma; Childhood Supratentorial Ependymoma; Newly Diagnosed Childhood Ependymoma; Recurrent Childhood Cerebellar Astrocytoma; Recurrent Childhood Cerebral Astrocytoma; Recurrent Childhood Ependymoma; Recurrent Childhood Medulloblastoma; Recurrent Childhood Supratentorial Primitive Neuroectodermal Tumor; Recurrent Childhood Visual Pathway and Hypothalamic Glioma; Recurrent Childhood Visual Pathway Glioma

The connections of layer 4 subdivisions in the primary visual cortex (V1) of the owl monkey.

PubMed

Boyd, J D; Mavity-Hudson, J A; Casagrande, V A

2000-07-01

The primary visual cortex (V1) of primates receives signals from parallel lateral geniculate nucleus (LGN) channels. These signals are utilized by the laminar and compartmental [i.e. cytochrome oxidase (CO) blob and interblob] circuitry of V1 to synthesize new output pathways appropriate for the next steps of analysis. Within this framework, this study had two objectives: (i) to analyze the con- nections between primary input and output layers and compartments of V1; and (ii) to determine differences in connection patterns that might be related to species differences in physiological properties in an effort to link specific pathways to visual functions. In this study we examined the intrinsic interlaminar connections of V1 in the owl monkey, a nocturnal New World monkey, with a special emphasis on the projections from layer 4 to layer 3. Interlaminar connections were labeled via small iontophoretic or pressure injections of tracers [horseradish peroxidase, biocytin, biotinylated dextrine amine (BDA) or cholera toxin subunit B conjugated to colloidal gold particles]. Our most significant finding was that layer 4 (4C of Brodmann) can be divided into three tiers based upon projections to the superficial layers. Specifically, we find that 4alpha (4Calpha), 4beta (4Cbeta) and 4ctr send primary projections to layers 3C (4B), 3Bbeta (4A) and 3Balpha (3B), respectively. Examination of laminar structure with Nissl staining supports a tripartite organization of layer 4. The cortical output layer above layer 3Balpha (3B) (e.g. layer 3A) does not appear to receive any direct connections from layer 4 but receives heavy input from layers 3Balpha (3B) and 3C (4B). Some connectional differences also were observed between the subdivisions of layer 3 and the infragranular layers. No consistent differences in connections were observed that distinguished CO blobs from interblobs or that could be correlated with differences in visual lifestyle (nocturnal versus diurnal) when compared with connectional data in other primates. Re-examination of data from previous studies in squirrel and macaque monkeys suggests that the tripartite organization of layer 4 and the unique projection pattern of layer 4ctr are not restricted to owl monkeys, but are common to a number of primate species.

VisualCNA: a GUI for interactive constraint network analysis and protein engineering for improving thermostability.

PubMed

Rathi, Prakash Chandra; Mulnaes, Daniel; Gohlke, Holger

2015-07-15

Constraint network analysis (CNA) is a graph theory-based rigidity analysis approach for linking a biomolecule's structure, flexibility, (thermo)stability and function. Results from CNA are highly information-rich and require intuitive, synchronized and interactive visualization for a comprehensive analysis. We developed VisualCNA, an easy-to-use PyMOL plug-in that allows setup of CNA runs and analysis of CNA results linking plots with molecular graphics representations. From a practical viewpoint, the most striking feature of VisualCNA is that it facilitates interactive protein engineering aimed at improving thermostability. VisualCNA and its dependencies (CNA and FIRST software) are available free of charge under GPL and academic licenses, respectively. VisualCNA and CNA are available at http://cpclab.uni-duesseldorf.de/software; FIRST is available at http://flexweb.asu.edu. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Correspondence between visual and electrical input filters of ON and OFF mouse retinal ganglion cells

NASA Astrophysics Data System (ADS)

Sekhar, S.; Jalligampala, A.; Zrenner, E.; Rathbun, D. L.

2017-08-01

Objective. Over the past two decades retinal prostheses have made major strides in restoring functional vision to patients blinded by diseases such as retinitis pigmentosa. Presently, implants use single pulses to activate the retina. Though this stimulation paradigm has proved beneficial to patients, an unresolved problem is the inability to selectively stimulate the on and off visual pathways. To this end our goal was to test, using white noise, voltage-controlled, cathodic, monophasic pulse stimulation, whether different retinal ganglion cell (RGC) types in the wild type retina have different electrical input filters. This is an important precursor to addressing pathway-selective stimulation. Approach. Using full-field visual flash and electrical and visual Gaussian noise stimulation, combined with the technique of spike-triggered averaging (STA), we calculate the electrical and visual input filters for different types of RGCs (classified as on, off or on-off based on their response to the flash stimuli). Main results. Examining the STAs, we found that the spiking activity of on cells during electrical stimulation correlates with a decrease in the voltage magnitude preceding a spike, while the spiking activity of off cells correlates with an increase in the voltage preceding a spike. No electrical preference was found for on-off cells. Comparing STAs of wild type and rd10 mice revealed narrower electrical STA deflections with shorter latencies in rd10. Significance. This study is the first comparison of visual cell types and their corresponding temporal electrical input filters in the retina. The altered input filters in degenerated rd10 retinas are consistent with photoreceptor stimulation underlying visual type-specific electrical STA shapes in wild type retina. It is therefore conceivable that existing implants could target partially degenerated photoreceptors that have only lost their outer segments, but not somas, to selectively activate the on and off visual pathways.

Disentangling fine motor skills' relations to academic achievement: the relative contributions of visual-spatial integration and visual-motor coordination.

PubMed

Carlson, Abby G; Rowe, Ellen; Curby, Timothy W

2013-01-01

Recent research has established a connection between children's fine motor skills and their academic performance. Previous research has focused on fine motor skills measured prior to elementary school, while the present sample included children ages 5-18 years old, making it possible to examine whether this link remains relevant throughout childhood and adolescence. Furthermore, the majority of research linking fine motor skills and academic achievement has not determined which specific components of fine motor skill are driving this relation. The few studies that have looked at associations of separate fine motor tasks with achievement suggest that copying tasks that tap visual-spatial integration skills are most closely related to achievement. The present study examined two separate elements of fine motor skills--visual-motor coordination and visual-spatial integration--and their associations with various measures of academic achievement. Visual-motor coordination was measured using tracing tasks, while visual-spatial integration was measured using copy-a-figure tasks. After controlling for gender, socioeconomic status, IQ, and visual-motor coordination, and visual-spatial integration explained significant variance in children's math and written expression achievement. Knowing that visual-spatial integration skills are associated with these two achievement domains suggests potential avenues for targeted math and writing interventions for children of all ages.

Developmental dyslexia: exploring how much phonological and visual attention span disorders are linked to simultaneous auditory processing deficits.

PubMed

Lallier, Marie; Donnadieu, Sophie; Valdois, Sylviane

2013-07-01

The simultaneous auditory processing skills of 17 dyslexic children and 17 skilled readers were measured using a dichotic listening task. Results showed that the dyslexic children exhibited difficulties reporting syllabic material when presented simultaneously. As a measure of simultaneous visual processing, visual attention span skills were assessed in the dyslexic children. We presented the dyslexic children with a phonological short-term memory task and a phonemic awareness task to quantify their phonological skills. Visual attention spans correlated positively with individual scores obtained on the dichotic listening task while phonological skills did not correlate with either dichotic scores or visual attention span measures. Moreover, all the dyslexic children with a dichotic listening deficit showed a simultaneous visual processing deficit, and a substantial number of dyslexic children exhibited phonological processing deficits whether or not they exhibited low dichotic listening scores. These findings suggest that processing simultaneous auditory stimuli may be impaired in dyslexic children regardless of phonological processing difficulties and be linked to similar problems in the visual modality.

The Verriest Lecture: Color lessons from space, time, and motion

PubMed Central

Shevell, Steven K.

2012-01-01

The appearance of a chromatic stimulus depends on more than the wavelengths composing it. The scientific literature has countless examples showing that spatial and temporal features of light influence the colors we see. Studying chromatic stimuli that vary over space, time or direction of motion has a further benefit beyond predicting color appearance: the unveiling of otherwise concealed neural processes of color vision. Spatial or temporal stimulus variation uncovers multiple mechanisms of brightness and color perception at distinct levels of the visual pathway. Spatial variation in chromaticity and luminance can change perceived three-dimensional shape, an example of chromatic signals that affect a percept other than color. Chromatic objects in motion expose the surprisingly weak link between the chromaticity of objects and their physical direction of motion, and the role of color in inducing an illusory motion direction. Space, time and motion – color’s colleagues – reveal the richness of chromatic neural processing. PMID:22330398

Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells

PubMed Central

Johard, Helena; Mahdessian, Diana; Fedr, Radek; Marks, Carolyn; Medalová, Jiřina; Souček, Karel; Lundberg, Emma; Linnarsson, Sten; Bryja, Vítězslav; Sekyrova, Petra; Altun, Mikael; Andäng, Michael

2017-01-01

The cell cycle coordinates core functions such as replication and cell division. However, cell-cycle-regulated transcription in the control of non-core functions, such as cell identity maintenance through specific transcription factors (TFs) and signalling pathways remains unclear. Here, we provide a resource consisting of mapped transcriptomes in unsynchronized HeLa and U2OS cancer cells sorted for cell cycle phase by Fucci reporter expression. We developed a novel algorithm for data analysis that enables efficient visualization and data comparisons and identified cell cycle synchronization of Notch signalling and TFs associated with development. Furthermore, the cell cycle synchronizes with the circadian clock, providing a possible link between developmental transcriptional networks and the cell cycle. In conclusion we find that cell cycle synchronized transcriptional patterns are temporally compartmentalized and more complex than previously anticipated, involving genes, which control cell identity and development. PMID:29228002

Sensory maps in the claustrum of the cat.

PubMed

Olson, C R; Graybiel, A M

1980-12-04

The claustrum is a telencephalic cell group (Fig. 1A, B) possessing widespread reciprocal connections with the neocortex. In this regard, it bears a unique and striking resemblance to the thalamus. We have now examined the anatomical ordering of pathways linking the claustrum with sensory areas of the cat neocortex and, in parallel electrophysiological experiments, have studied the functional organization of claustral sensory zones so identified. Our findings indicate that there are discrete visual and somatosensory subdivisions in the claustrum interconnected with the corresponding primary sensory areas of the neocortex and that the respective zones contain orderly retinotopic and somatotopic maps. A third claustral region receiving fibre projections from the auditory cortex in or near area Ep was found to contain neurones responsive to auditory stimulation. We conclude that loops connecting sensory areas of the neocortex with satellite zones in the claustrum contribute to the early processing of exteroceptive information by the forebrain.

An assessment of molecular pathways of obesity susceptible to nutrient, toxicant and genetically induced epigenetic perturbation

PubMed Central

Xue, Jing; Ideraabdullah, Folami Y.

2015-01-01

In recent years, the etiology of human disease has greatly improved with the inclusion of epigenetic mechanisms, in particular as a common link between environment and disease. However, for most diseases we lack a detailed interpretation of the epigenetic regulatory pathways perturbed by environment and causal mechanisms. Here, we focus on recent findings elucidating nutrient-related epigenetic changes linked to obesity. We highlight studies demonstrating that obesity is a complex disease linked to disruption of epigenetically regulated metabolic pathways in the brain, adipose tissue and liver. These pathways regulate (1) homeostatic and hedonic eating behaviors (2) adipocyte differentiation and fat accumulation, and (3) energy expenditure. By compiling these data we illustrate that obesity-related phenotypes are repeatedly linked to disruption of critical epigenetic mechanisms that regulate of key metabolic genes. These data are supported by genetic mutation of key epigenetic regulators and many of the diet induced epigenetic mechanisms of obesity are also perturbed by exposure to environmental toxicants. Identifying similarly perturbed epigenetic mechanisms in multiple experimental models of obesity strengthens the translational applications of these findings. We also discuss many of the ongoing challenges to understanding the role of environmentally-induced epigenetic pathways in obesity and suggest future studies to elucidate these roles. This assessment illustrates our current understanding of molecular pathways of obesity that are susceptible to environmental perturbation via epigenetic mechanisms. Thus, it lays the groundwork for dissecting the complex interactions between diet, genes, and toxicants that contribute to obesity and obesity-related phenotypes. PMID:27012616

Age, Sex, and Verbal Abilities Affect Location of Linguistic Connectivity in Ventral Visual Pathway

ERIC Educational Resources Information Center

Burman, Douglas D.; Minas, Taylor; Bolger, Donald J.; Booth, James R.

2013-01-01

Previous studies have shown that the "strength" of connectivity between regions can vary depending upon the cognitive demands of a task. In this study, the "location" of task-dependent connectivity from the primary visual cortex (V1) was examined in 43 children (ages 9-15) performing visual tasks; connectivity maxima were identified for a visual…

NaviCell Web Service for network-based data visualization.

PubMed

Bonnet, Eric; Viara, Eric; Kuperstein, Inna; Calzone, Laurence; Cohen, David P A; Barillot, Emmanuel; Zinovyev, Andrei

2015-07-01

Data visualization is an essential element of biological research, required for obtaining insights and formulating new hypotheses on mechanisms of health and disease. NaviCell Web Service is a tool for network-based visualization of 'omics' data which implements several data visual representation methods and utilities for combining them together. NaviCell Web Service uses Google Maps and semantic zooming to browse large biological network maps, represented in various formats, together with different types of the molecular data mapped on top of them. For achieving this, the tool provides standard heatmaps, barplots and glyphs as well as the novel map staining technique for grasping large-scale trends in numerical values (such as whole transcriptome) projected onto a pathway map. The web service provides a server mode, which allows automating visualization tasks and retrieving data from maps via RESTful (standard HTTP) calls. Bindings to different programming languages are provided (Python and R). We illustrate the purpose of the tool with several case studies using pathway maps created by different research groups, in which data visualization provides new insights into molecular mechanisms involved in systemic diseases such as cancer and neurodegenerative diseases. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Visualizing Volcanic Clouds in the Atmosphere and Their Impact on Air Traffic.

PubMed

Gunther, Tobias; Schulze, Maik; Friederici, Anke; Theisel, Holger

2016-01-01

Volcanic eruptions are not only hazardous in the direct vicinity of a volcano, but they also affect the climate and air travel for great distances. This article sheds light on the Grímsvötn, Puyehue-Cordón Caulle, and Nabro eruptions in 2011. The authors study the agreement of the complementary satellite data, reconstruct sulfate aerosol and volcanic ash clouds, visualize endangered flight routes, minimize occlusion in particle trajectory visualizations, and focus on the main pathways of Nabro's sulfate aerosol into the stratosphere. The results here were developed for the 2014 IEEE Scientific Visualization Contest, which centers around the fusion of multiple satellite data modalities to reconstruct and assess the movement of volcanic ash and sulfate aerosol emissions. Using data from three volcanic eruptions that occurred in the span of approximately three weeks, the authors study the agreement of the complementary satellite data, reconstruct sulfate aerosol and volcanic ash clouds, visualize endangered flight routes, minimize occlusion in particle trajectory visualizations, and focus on the main pathways of sulfate aerosol into the stratosphere. This video provides animations of the reconstructed ash clouds. https://youtu.be/D9DvJ5AvZAs.

NaviCell Web Service for network-based data visualization

PubMed Central

Bonnet, Eric; Viara, Eric; Kuperstein, Inna; Calzone, Laurence; Cohen, David P. A.; Barillot, Emmanuel; Zinovyev, Andrei

2015-01-01

Data visualization is an essential element of biological research, required for obtaining insights and formulating new hypotheses on mechanisms of health and disease. NaviCell Web Service is a tool for network-based visualization of ‘omics’ data which implements several data visual representation methods and utilities for combining them together. NaviCell Web Service uses Google Maps and semantic zooming to browse large biological network maps, represented in various formats, together with different types of the molecular data mapped on top of them. For achieving this, the tool provides standard heatmaps, barplots and glyphs as well as the novel map staining technique for grasping large-scale trends in numerical values (such as whole transcriptome) projected onto a pathway map. The web service provides a server mode, which allows automating visualization tasks and retrieving data from maps via RESTful (standard HTTP) calls. Bindings to different programming languages are provided (Python and R). We illustrate the purpose of the tool with several case studies using pathway maps created by different research groups, in which data visualization provides new insights into molecular mechanisms involved in systemic diseases such as cancer and neurodegenerative diseases. PMID:25958393

Delayed visual maturation in infants: a disorder of figure-ground separation?

PubMed

Harris, C M; Kriss, A; Shawkat, F; Taylor, D; Russell-Eggitt, I

1996-01-01

Delayed visual maturation (DVM) is characterised by visual unresponsiveness in early infancy, which subsequently improves spontaneously to normal levels. We studied the optokinetic response and recorded pattern reversal VEPs in six infants with DVM (aged 2-4 months) when they were at the stage of complete visual unresponsiveness. Although no saccades or visual tracking with the eyes or head could be elicited to visual objects, a normal full-field rapid buildup OKN response occurred when viewing biocularly or during monocular stimulation in the temporo-nasal direction of the viewing eye. Almost no monocular OKN could be elicited in the naso-temporal direction, which was significantly poorer than normal age-matched infants. No OKN quick phases were missed, and there were no other signs of "ocular motor apraxia." VEPs were normal in amplitude and latency for age. It appears, therefore, that infants with DVM are delayed in orienting to local regions of the visual field, but can respond to full-field motion. The presence of normal OKN quick-phases and slow-phases suggests normal brain stem function, and the presence of normal pattern VEPs suggests a normal retino-geniculo-striate pathway. These oculomotor and electrophysiological findings suggest delayed development of extra-striate cortical structures, possibly involving either an abnormality in figure-ground segregation or in attentional pathways.

Altered functional connectivity in lesional peduncular hallucinosis with REM sleep behavior disorder.

PubMed

Geddes, Maiya R; Tie, Yanmei; Gabrieli, John D E; McGinnis, Scott M; Golby, Alexandra J; Whitfield-Gabrieli, Susan

2016-01-01

Brainstem lesions causing peduncular hallucinosis (PH) produce vivid visual hallucinations occasionally accompanied by sleep disorders. Overlapping brainstem regions modulate visual pathways and REM sleep functions via gating of thalamocortical networks. A 66-year-old man with paroxysmal atrial fibrillation developed abrupt-onset complex visual hallucinations with preserved insight and violent dream enactment behavior. Brain MRI showed restricted diffusion in the left rostrodorsal pons suggestive of an acute ischemic stroke. REM sleep behavior disorder (RBD) was diagnosed on polysomnography. We investigated the integrity of ponto-geniculate-occipital circuits with seed-based resting-state functional connectivity MRI (rs-fcMRI) in this patient compared to 46 controls. Rs-fcMRI revealed significantly reduced functional connectivity between the lesion and lateral geniculate nuclei (LGN), and between LGN and visual association cortex compared to controls. Conversely, functional connectivity between brainstem and visual association cortex, and between visual association cortex and prefrontal cortex (PFC) was significantly increased in the patient. Focal damage to the rostrodorsal pons is sufficient to cause RBD and PH in humans, suggesting an overlapping mechanism in both syndromes. This lesion produced a pattern of altered functional connectivity consistent with disrupted visual cortex connectivity via de-afferentation of thalamocortical pathways. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Long genes and genes with multiple splice variants are enriched in pathways linked to cancer and other multigenic diseases.

PubMed

Sahakyan, Aleksandr B; Balasubramanian, Shankar

2016-03-12

The role of random mutations and genetic errors in defining the etiology of cancer and other multigenic diseases has recently received much attention. With the view that complex genes should be particularly vulnerable to such events, here we explore the link between the simple properties of the human genes, such as transcript length, number of splice variants, exon/intron composition, and their involvement in the pathways linked to cancer and other multigenic diseases. We reveal a substantial enrichment of cancer pathways with long genes and genes that have multiple splice variants. Although the latter two factors are interdependent, we show that the overall gene length and splicing complexity increase in cancer pathways in a partially decoupled manner. Our systematic survey for the pathways enriched with top lengthy genes and with genes that have multiple splice variants reveal, along with cancer pathways, the pathways involved in various neuronal processes, cardiomyopathies and type II diabetes. We outline a correlation between the gene length and the number of somatic mutations. Our work is a step forward in the assessment of the role of simple gene characteristics in cancer and a wider range of multigenic diseases. We demonstrate a significant accumulation of long genes and genes with multiple splice variants in pathways of multigenic diseases that have already been associated with de novo mutations. Unlike the cancer pathways, we note that the pathways of neuronal processes, cardiomyopathies and type II diabetes contain genes long enough for topoisomerase-dependent gene expression to also be a potential contributing factor in the emergence of pathologies, should topoisomerases become impaired.

[Parasites and cancer: is there a causal link?

PubMed

Cheeseman, Kevin; Certad, Gabriela; Weitzman, Jonathan B

2016-10-01

Over 20 % of cancers have infectious origins, including well-known examples of microbes such as viruses (HPV, EBV) and bacteria (H. pylori). The contribution of intracellular eukaryotic parasites to cancer etiology is largely unexplored. Epidemiological and clinical reports indicate that eukaryotic protozoan, such as intracellular apicomplexan that cause diseases of medical or economic importance, can be linked to various cancers: Theileria and Cryptosporidium induce host cell transformation while Plasmodium was linked epidemiologically to the "African lymphoma belt" over fifty years ago. These intracellular eukaryotic parasites hijack cellular pathways to manipulate the host cell epigenome, cellular machinery, signaling pathways and epigenetic programs and marks, such as methylation and acetylation, for their own benefit. In doing so, they tinker with the same pathways as those deregulated during cancer onset. Here we discuss how epidemiological evidence linking eukaryotic intracellular parasites to cancer onset are further strengthened by recent mechanistic studies in three apicomplexan parasites. © 2016 médecine/sciences – Inserm.

Exploring the Climate Change, Migration and Conflict Nexus.

PubMed

Burrows, Kate; Kinney, Patrick L

2016-04-22

The potential link between climate change, migration, and conflict has been widely discussed and is increasingly viewed by policy makers as a security issue. However, considerable uncertainty remains regarding the role that climate variability and change play among the many drivers of migration and conflict. The overall objective of this paper is to explore the potential pathways linking climate change, migration and increased risk of conflict. We review the existing literature surrounding this issue and break the problem into two components: the links between climate change and migration, and those between migration and conflict. We found a large range of views regarding the importance of climate change as a driver for increasing rates of migration and subsequently of conflict. We argue that future research should focus not only on the climate-migration-conflict pathway but also work to understand the other pathways by which climate variability and change might exacerbate conflict. We conclude by proposing five questions to help guide future research on the link between climate change, migration, and conflict.

Exploring the Climate Change, Migration and Conflict Nexus

PubMed Central

Burrows, Kate; Kinney, Patrick L.

2016-01-01

The potential link between climate change, migration, and conflict has been widely discussed and is increasingly viewed by policy makers as a security issue. However, considerable uncertainty remains regarding the role that climate variability and change play among the many drivers of migration and conflict. The overall objective of this paper is to explore the potential pathways linking climate change, migration and increased risk of conflict. We review the existing literature surrounding this issue and break the problem into two components: the links between climate change and migration, and those between migration and conflict. We found a large range of views regarding the importance of climate change as a driver for increasing rates of migration and subsequently of conflict. We argue that future research should focus not only on the climate-migration-conflict pathway but also work to understand the other pathways by which climate variability and change might exacerbate conflict. We conclude by proposing five questions to help guide future research on the link between climate change, migration, and conflict. PMID:27110806

Pathways linking parental divorce with adolescent depression.

PubMed

Aseltine, R H

1996-06-01

This article examines the intervening pathways linking parental divorce with adolescent depression, using both cross-sectional and prospective data from a study of high school students in the Boston metropolitan area. Overall, findings reveal that parental divorce is linked with adolescent depression in two ways: (1) it is a source of numerous secondary problems and stresses that are causally related to depression, and (2) it alters youths' reactivity to these stresses, in some cases enhancing, but in other cases mitigating, their depressive effects. Analyses demonstrated the central role of economic hardship in linking family status with depression, with the strength of this indirect pathway partly attributable to the greater vulnerability of youths in single-parent families to financial stresses. In contrast, family conflict did not account for the distress of youths in single-parent families, largely because of their immunity to the effects of such conflict. Finally, prospective data failed to support the hypothesis that differences between youths in single-parent and intact families predate the divorce.

HLB1 Is a Tetratricopeptide Repeat Domain-Containing Protein That Operates at the Intersection of the Exocytic and Endocytic Pathways at the TGN/EE in Arabidopsis

DOE PAGES

Sparks, J. Alan; Kwon, Taegun; Renna, Luciana; ...

2016-03-03

The endomembrane system plays essential roles in plant development, but the proteome responsible for its function and organization remains largely uncharacterized in plants. For this study, we identified and characterized the HYPERSENSITIVE TO LATRUNCULIN B1 (HLB1) protein isolated through a forward-genetic screen in Arabidopsis thaliana for mutants with heightened sensitivity to actin-disrupting drugs. HLB1 is a plant-specific tetratricopeptide repeat domain-containing protein of unknown function encoded by a single Arabidopsis gene. HLB1 associated with the trans-Golgi network (TGN)/early endosome (EE) and tracked along filamentous actin, indicating that it could link post-Golgi traffic with the actin cytoskeleton in plants. HLB1 was foundmore » to interact with the ADP-ribosylation-factor guanine nucleotide exchange factor, MIN7/BEN1 (HOPM INTERACTOR7/BREFELDIN A-VISUALIZED ENDOCYTIC TRAFFICKING DEFECTIVE1) by coimmunoprecipitation. The min7/ben1 mutant phenocopied the mild root developmental defects and latrunculin B hypersensitivity of hlb1, and analyses of a hlb1/ min7/ben1 double mutant showed that hlb1 and min7/ben1 operate in common genetic pathways. Based on these data, we propose that HLB1 together with MIN7/BEN1 form a complex with actin to modulate the function of the TGN/EE at the intersection of the exocytic and endocytic pathways in plants.« less

How might contact with nature promote human health? Promising mechanisms and a possible central pathway.

PubMed

Kuo, Ming

2015-01-01

How might contact with nature promote human health? Myriad studies have linked the two; at this time the task of identifying the mechanisms underlying this link is paramount. This article offers: (1) a compilation of plausible pathways between nature and health; (2) criteria for identifying a possible central pathway; and (3) one promising candidate for a central pathway. The 21 pathways identified here include environmental factors, physiological and psychological states, and behaviors or conditions, each of which has been empirically tied to nature and has implications for specific physical and mental health outcomes. While each is likely to contribute to nature's impacts on health to some degree and under some circumstances, this paper explores the possibility of a central pathway by proposing criteria for identifying such a pathway and illustrating their use. A particular pathway is more likely to be central if it can account for the size of nature's impacts on health, account for nature's specific health outcomes, and subsume other pathways. By these criteria, enhanced immune functioning emerges as one promising candidate for a central pathway between nature and health. There may be others.

Employer-Led Organizations and Skill Supply Chains: Linking Worker Advancement with the Skill Needs of Employers. Issue Brief.

ERIC Educational Resources Information Center

Mills, Jack; Prince, Heath

Skill supply chains apply a chain strategy to human resources to make the labor market more efficient. They link the multiple skill levels in a given labor market within a network of recruitment pathways for employers and advancement pathways for workers. Skill supply chains are based on employers' actual skill needs and on the principle that…

Attentional enhancement of spatial resolution: linking behavioural and neurophysiological evidence

PubMed Central

Anton-Erxleben, Katharina; Carrasco, Marisa

2014-01-01

Attention allows us to select relevant sensory information for preferential processing. Behaviourally, it improves performance in various visual tasks. One prominent effect of attention is the modulation of performance in tasks that involve the visual system’s spatial resolution. Physiologically, attention modulates neuronal responses and alters the profile and position of receptive fields near the attended location. Here, we develop a hypothesis linking the behavioural and electrophysiological evidence. The proposed framework seeks to explain how these receptive field changes enhance the visual system’s effective spatial resolution and how the same mechanisms may also underlie attentional effects on the representation of spatial information. PMID:23422910

Ability of Mn2+ to Permeate the Eye and Availability of Manganese-enhanced Magnetic Resonance Imaging for Visual Pathway Imaging via Topical Administration

PubMed Central

Chen, Yao; Shi, Chun-Yan; Li, Ying; Hu, Yun-Tao; Han, Hong-Bin; Sun, Xiao-Dong; Salvi, Satyajeet S; Ma, Zhi-Zhong

2016-01-01

Background: Manganese-enhanced magnetic resonance imaging (MEMRI) for visual pathway imaging via topical administration requires further research. This study investigated the permeability of the corneal epithelium and corneal toxicity after topical administration of Mn2+ to understand the applicability of MEMRI. Methods: Forty New Zealand rabbits were divided into 0.05 mol/L, 0.10 mol/L, and 0.20 mol/L groups as well as a control group (n = 10 in each group). Each group was further subdivided into epithelium-removed and epithelium-intact subgroups (n = 5 in each subgroup). Rabbits were given 8 drops of MnCl2 in 5 min intervals. The Mn2+ concentrations in the aqueous and vitreous humors were analyzed using inductively coupled plasma-mass spectrometry at different time points. MEMRI scanning was carried out to image the visual pathway after 24 h. The corneal toxicity of Mn2+ was evaluated with corneal imaging and pathology slices. Results: Between the aqueous and vitreous humors, there was a 10 h lag for the peak Mn2+ concentration times. The intraocular Mn2+ concentration increased with the concentration gradients of Mn2+ and was higher in the epithelium-removed subgroup than that in the epithelium-intact subgroup. The enhancement of the visual pathway was achieved in the 0.10 mol/L and 0.20 mol/L epithelium-removed subgroups. The corresponding peak concentrations of Mn2+ were 5087 ± 666 ng/ml, 22920 ± 1188 ng/ml in the aqueous humor and 884 ± 78 ng/ml, 2556 ± 492 ng/ml in the vitreous body, respectively. Corneal injury was evident in the epithelium-removed and 0.20 mol/L epithelium-intact subgroups. Conclusions: The corneal epithelium is a barrier to Mn2+, and the iris and lens septum might be another intraocular barrier to the permeation of Mn2+. An elevated Mn2+ concentration contributes to the increased permeation of Mn2+, higher MEMRI signal, and corneal toxicity. The enhancement of the visual pathway requires an effective Mn2+ concentration in the vitreous body. PMID:27453232

"The Mask Who Wasn't There": Visual Masking Effect with the Perceptual Absence of the Mask

ERIC Educational Resources Information Center

Rey, Amandine Eve; Riou, Benoit; Muller, Dominique; Dabic, Stéphanie; Versace, Rémy

2015-01-01

Does a visual mask need to be perceptually present to disrupt processing? In the present research, we proposed to explore the link between perceptual and memory mechanisms by demonstrating that a typical sensory phenomenon (visual masking) can be replicated at a memory level. Experiment 1 highlighted an interference effect of a visual mask on the…

Do we track what we see? Common versus independent processing for motion perception and smooth pursuit eye movements: a review.

PubMed

Spering, Miriam; Montagnini, Anna

2011-04-22

Many neurophysiological studies in monkeys have indicated that visual motion information for the guidance of perception and smooth pursuit eye movements is - at an early stage - processed in the same visual pathway in the brain, crucially involving the middle temporal area (MT). However, these studies left some questions unanswered: Are perception and pursuit driven by the same or independent neuronal signals within this pathway? Are the perceptual interpretation of visual motion information and the motor response to visual signals limited by the same source of neuronal noise? Here, we review psychophysical studies that were motivated by these questions and compared perception and pursuit behaviorally in healthy human observers. We further review studies that focused on the interaction between perception and pursuit. The majority of results point to similarities between perception and pursuit, but dissociations were also reported. We discuss recent developments in this research area and conclude with suggestions for common and separate principles for the guidance of perceptual and motor responses to visual motion information. Copyright © 2010 Elsevier Ltd. All rights reserved.

O-linked β-N-acetylglucosamine transferase directs cell proliferation in idiopathic pulmonary arterial hypertension.

PubMed

Barnes, Jarrod W; Tian, Liping; Heresi, Gustavo A; Farver, Carol F; Asosingh, Kewal; Comhair, Suzy A A; Aulak, Kulwant S; Dweik, Raed A

2015-04-07

Idiopathic pulmonary arterial hypertension (IPAH) is a cardiopulmonary disease characterized by cellular proliferation and vascular remodeling. A more recently recognized characteristic of the disease is the dysregulation of glucose metabolism. The primary link between altered glucose metabolism and cell proliferation in IPAH has not been elucidated. We aimed to determine the relationship between glucose metabolism and smooth muscle cell proliferation in IPAH. Human IPAH and control patient lung tissues and pulmonary artery smooth muscle cells (PASMCs) were used to analyze a specific pathway of glucose metabolism, the hexosamine biosynthetic pathway. We measured the levels of O-linked β-N-acetylglucosamine modification, O-linked β-N-acetylglucosamine transferase (OGT), and O-linked β-N-acetylglucosamine hydrolase in control and IPAH cells and tissues. Our data suggest that the activation of the hexosamine biosynthetic pathway directly increased OGT levels and activity, triggering changes in glycosylation and PASMC proliferation. Partial knockdown of OGT in IPAH PASMCs resulted in reduced global O-linked β-N-acetylglucosamine modification levels and abrogated PASMC proliferation. The increased proliferation observed in IPAH PASMCs was directly impacted by proteolytic activation of the cell cycle regulator, host cell factor-1. Our data demonstrate that hexosamine biosynthetic pathway flux is increased in IPAH and drives OGT-facilitated PASMC proliferation through specific proteolysis and direct activation of host cell factor-1. These findings establish a novel regulatory role for OGT in IPAH, shed a new light on our understanding of the disease pathobiology, and provide opportunities to design novel therapeutic strategies for IPAH. © 2015 American Heart Association, Inc.

Visual pathways from the perspective of cost functions and multi-task deep neural networks.

PubMed

Scholte, H Steven; Losch, Max M; Ramakrishnan, Kandan; de Haan, Edward H F; Bohte, Sander M

2018-01-01

Vision research has been shaped by the seminal insight that we can understand the higher-tier visual cortex from the perspective of multiple functional pathways with different goals. In this paper, we try to give a computational account of the functional organization of this system by reasoning from the perspective of multi-task deep neural networks. Machine learning has shown that tasks become easier to solve when they are decomposed into subtasks with their own cost function. We hypothesize that the visual system optimizes multiple cost functions of unrelated tasks and this causes the emergence of a ventral pathway dedicated to vision for perception, and a dorsal pathway dedicated to vision for action. To evaluate the functional organization in multi-task deep neural networks, we propose a method that measures the contribution of a unit towards each task, applying it to two networks that have been trained on either two related or two unrelated tasks, using an identical stimulus set. Results show that the network trained on the unrelated tasks shows a decreasing degree of feature representation sharing towards higher-tier layers while the network trained on related tasks uniformly shows high degree of sharing. We conjecture that the method we propose can be used to analyze the anatomical and functional organization of the visual system and beyond. We predict that the degree to which tasks are related is a good descriptor of the degree to which they share downstream cortical-units. Copyright © 2017 Elsevier Ltd. All rights reserved.

Joint Attention without Gaze Following: Human Infants and Their Parents Coordinate Visual Attention to Objects through Eye-Hand Coordination

PubMed Central

Yu, Chen; Smith, Linda B.

2013-01-01

The coordination of visual attention among social partners is central to many components of human behavior and human development. Previous research has focused on one pathway to the coordination of looking behavior by social partners, gaze following. The extant evidence shows that even very young infants follow the direction of another's gaze but they do so only in highly constrained spatial contexts because gaze direction is not a spatially precise cue as to the visual target and not easily used in spatially complex social interactions. Our findings, derived from the moment-to-moment tracking of eye gaze of one-year-olds and their parents as they actively played with toys, provide evidence for an alternative pathway, through the coordination of hands and eyes in goal-directed action. In goal-directed actions, the hands and eyes of the actor are tightly coordinated both temporally and spatially, and thus, in contexts including manual engagement with objects, hand movements and eye movements provide redundant information about where the eyes are looking. Our findings show that one-year-olds rarely look to the parent's face and eyes in these contexts but rather infants and parents coordinate looking behavior without gaze following by attending to objects held by the self or the social partner. This pathway, through eye-hand coupling, leads to coordinated joint switches in visual attention and to an overall high rate of looking at the same object at the same time, and may be the dominant pathway through which physically active toddlers align their looking behavior with a social partner. PMID:24236151

Differentiating pathway-specific from non-specific effects in high-throughput toxicity data: A foundation for prioritizing adverse outcome pathway development

EPA Science Inventory

The U.S. Environmental Protection Agency’s ToxCast program has screened thousands of chemicals for biological activity, primarily using high-throughput in vitro bioassays. Adverse outcome pathways (AOPs) offer a means to link pathway-specific biological activities with pote...

Service-based analysis of biological pathways

PubMed Central

Zheng, George; Bouguettaya, Athman

2009-01-01

Background Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at achieving either objective, but not both. Such limitations can be effectively tackled leveraging a Web service-based modeling and mining approach. Results Inspired by molecular recognitions and drug discovery processes, we developed a Web service mining tool, named PathExplorer, to discover potentially interesting biological pathways linking service models of biological processes. The tool uses an innovative approach to identify useful pathways based on graph-based hints and service-based simulation verifying user's hypotheses. Conclusion Web service modeling of biological processes allows the easy access and invocation of these processes on the Web. Web service mining techniques described in this paper enable the discovery of biological pathways linking these process service models. Algorithms presented in this paper for automatically highlighting interesting subgraph within an identified pathway network enable the user to formulate hypothesis, which can be tested out using our simulation algorithm that are also described in this paper. PMID:19796403

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data

PubMed Central

2016-01-01

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app. PMID:27302480

ProXL (Protein Cross-Linking Database): A Platform for Analysis, Visualization, and Sharing of Protein Cross-Linking Mass Spectrometry Data.

PubMed

Riffle, Michael; Jaschob, Daniel; Zelter, Alex; Davis, Trisha N

2016-08-05

ProXL is a Web application and accompanying database designed for sharing, visualizing, and analyzing bottom-up protein cross-linking mass spectrometry data with an emphasis on structural analysis and quality control. ProXL is designed to be independent of any particular software pipeline. The import process is simplified by the use of the ProXL XML data format, which shields developers of data importers from the relative complexity of the relational database schema. The database and Web interfaces function equally well for any software pipeline and allow data from disparate pipelines to be merged and contrasted. ProXL includes robust public and private data sharing capabilities, including a project-based interface designed to ensure security and facilitate collaboration among multiple researchers. ProXL provides multiple interactive and highly dynamic data visualizations that facilitate structural-based analysis of the observed cross-links as well as quality control. ProXL is open-source, well-documented, and freely available at https://github.com/yeastrc/proxl-web-app .

CLMSVault: A Software Suite for Protein Cross-Linking Mass-Spectrometry Data Analysis and Visualization.

PubMed

Courcelles, Mathieu; Coulombe-Huntington, Jasmin; Cossette, Émilie; Gingras, Anne-Claude; Thibault, Pierre; Tyers, Mike

2017-07-07

Protein cross-linking mass spectrometry (CL-MS) enables the sensitive detection of protein interactions and the inference of protein complex topology. The detection of chemical cross-links between protein residues can identify intra- and interprotein contact sites or provide physical constraints for molecular modeling of protein structure. Recent innovations in cross-linker design, sample preparation, mass spectrometry, and software tools have significantly improved CL-MS approaches. Although a number of algorithms now exist for the identification of cross-linked peptides from mass spectral data, a dearth of user-friendly analysis tools represent a practical bottleneck to the broad adoption of the approach. To facilitate the analysis of CL-MS data, we developed CLMSVault, a software suite designed to leverage existing CL-MS algorithms and provide intuitive and flexible tools for cross-platform data interpretation. CLMSVault stores and combines complementary information obtained from different cross-linkers and search algorithms. CLMSVault provides filtering, comparison, and visualization tools to support CL-MS analyses and includes a workflow for label-free quantification of cross-linked peptides. An embedded 3D viewer enables the visualization of quantitative data and the mapping of cross-linked sites onto PDB structural models. We demonstrate the application of CLMSVault for the analysis of a noncovalent Cdc34-ubiquitin protein complex cross-linked under different conditions. CLMSVault is open-source software (available at https://gitlab.com/courcelm/clmsvault.git ), and a live demo is available at http://democlmsvault.tyerslab.com/ .

Visual Links: Discovery in Art and Science.

ERIC Educational Resources Information Center

Dake, Dennis M.

Some specific aspects of the process of discovery are explored as they are experienced in the visual arts and the physical sciences. Both fields use the same visual/brain processing system, and both disciplines share an imaginative and productive interest in the disciplined use of imagistic thinking. Many productive interactions between visual…

Visual Memory for Objects Following Foveal Vision Loss

ERIC Educational Resources Information Center

Geringswald, Franziska; Herbik, Anne; Hofmüller, Wolfram; Hoffmann, Michael B.; Pollmann, Stefan

2015-01-01

Allocation of visual attention is crucial for encoding items into visual long-term memory. In free vision, attention is closely linked to the center of gaze, raising the question whether foveal vision loss entails suboptimal deployment of attention and subsequent impairment of object encoding. To investigate this question, we examined visual…

Are Deaf Students Visual Learners?

ERIC Educational Resources Information Center

Marschark, Marc; Morrison, Carolyn; Lukomski, Jennifer; Borgna, Georgianna; Convertino, Carol

2013-01-01

It is frequently assumed that by virtue of their hearing losses, deaf students are visual learners. Deaf individuals have some visual-spatial advantages relative to hearing individuals, but most have been linked to use of sign language rather than auditory deprivation. How such cognitive differences might affect academic performance has been…

Groups: knowledge spreadsheets for symbolic biocomputing.

PubMed

Travers, Michael; Paley, Suzanne M; Shrager, Jeff; Holland, Timothy A; Karp, Peter D

2013-01-01

Knowledge spreadsheets (KSs) are a visual tool for interactive data analysis and exploration. They differ from traditional spreadsheets in that rather than being oriented toward numeric data, they work with symbolic knowledge representation structures and provide operations that take into account the semantics of the application domain. 'Groups' is an implementation of KSs within the Pathway Tools system. Groups allows Pathway Tools users to define a group of objects (e.g. groups of genes or metabolites) from a Pathway/Genome Database. Groups can be transformed (e.g. by transforming a metabolite group to the group of pathways in which those metabolites are substrates); combined through set operations; analysed (e.g. through enrichment analysis); and visualized (e.g. by painting onto a metabolic map diagram). Users of the Pathway Tools-based BioCyc.org website have made extensive use of Groups, and an informal survey of Groups users suggests that Groups has achieved the goal of allowing biologists themselves to perform some data manipulations that previously would have required the assistance of a programmer. Database URL: BioCyc.org.

First-Pass Processing of Value Cues in the Ventral Visual Pathway.

PubMed

Sasikumar, Dennis; Emeric, Erik; Stuphorn, Veit; Connor, Charles E

2018-02-19

Real-world value often depends on subtle, continuously variable visual cues specific to particular object categories, like the tailoring of a suit, the condition of an automobile, or the construction of a house. Here, we used microelectrode recording in behaving monkeys to test two possible mechanisms for category-specific value-cue processing: (1) previous findings suggest that prefrontal cortex (PFC) identifies object categories, and based on category identity, PFC could use top-down attentional modulation to enhance visual processing of category-specific value cues, providing signals to PFC for calculating value, and (2) a faster mechanism would be first-pass visual processing of category-specific value cues, immediately providing the necessary visual information to PFC. This, however, would require learned mechanisms for processing the appropriate cues in a given object category. To test these hypotheses, we trained monkeys to discriminate value in four letter-like stimulus categories. Each category had a different, continuously variable shape cue that signified value (liquid reward amount) as well as other cues that were irrelevant. Monkeys chose between stimuli of different reward values. Consistent with the first-pass hypothesis, we found early signals for category-specific value cues in area TE (the final stage in monkey ventral visual pathway) beginning 81 ms after stimulus onset-essentially at the start of TE responses. Task-related activity emerged in lateral PFC approximately 40 ms later and consisted mainly of category-invariant value tuning. Our results show that, for familiar, behaviorally relevant object categories, high-level ventral pathway cortex can implement rapid, first-pass processing of category-specific value cues. Copyright © 2018 Elsevier Ltd. All rights reserved.

Visual Input to the Drosophila Central Complex by Developmentally and Functionally Distinct Neuronal Populations.

PubMed

Omoto, Jaison Jiro; Keleş, Mehmet Fatih; Nguyen, Bao-Chau Minh; Bolanos, Cheyenne; Lovick, Jennifer Kelly; Frye, Mark Arthur; Hartenstein, Volker

2017-04-24

The Drosophila central brain consists of stereotyped neural lineages, developmental-structural units of macrocircuitry formed by the sibling neurons of single progenitors called neuroblasts. We demonstrate that the lineage principle guides the connectivity and function of neurons, providing input to the central complex, a collection of neuropil compartments important for visually guided behaviors. One of these compartments is the ellipsoid body (EB), a structure formed largely by the axons of ring (R) neurons, all of which are generated by a single lineage, DALv2. Two further lineages, DALcl1 and DALcl2, produce neurons that connect the anterior optic tubercle, a central brain visual center, with R neurons. Finally, DALcl1/2 receive input from visual projection neurons of the optic lobe medulla, completing a three-legged circuit that we call the anterior visual pathway (AVP). The AVP bears a fundamental resemblance to the sky-compass pathway, a visual navigation circuit described in other insects. Neuroanatomical analysis and two-photon calcium imaging demonstrate that DALcl1 and DALcl2 form two parallel channels, establishing connections with R neurons located in the peripheral and central domains of the EB, respectively. Although neurons of both lineages preferentially respond to bright objects, DALcl1 neurons have small ipsilateral, retinotopically ordered receptive fields, whereas DALcl2 neurons share a large excitatory receptive field in the contralateral hemifield. DALcl2 neurons become inhibited when the object enters the ipsilateral hemifield and display an additional excitation after the object leaves the field of view. Thus, the spatial position of a bright feature, such as a celestial body, may be encoded within this pathway. Copyright © 2017 Elsevier Ltd. All rights reserved.

Population Coding of Visual Space: Comparison of Spatial Representations in Dorsal and Ventral Pathways

PubMed Central

Sereno, Anne B.; Lehky, Sidney R.

2011-01-01

Although the representation of space is as fundamental to visual processing as the representation of shape, it has received relatively little attention from neurophysiological investigations. In this study we characterize representations of space within visual cortex, and examine how they differ in a first direct comparison between dorsal and ventral subdivisions of the visual pathways. Neural activities were recorded in anterior inferotemporal cortex (AIT) and lateral intraparietal cortex (LIP) of awake behaving monkeys, structures associated with the ventral and dorsal visual pathways respectively, as a stimulus was presented at different locations within the visual field. In spatially selective cells, we find greater modulation of cell responses in LIP with changes in stimulus position. Further, using a novel population-based statistical approach (namely, multidimensional scaling), we recover the spatial map implicit within activities of neural populations, allowing us to quantitatively compare the geometry of neural space with physical space. We show that a population of spatially selective LIP neurons, despite having large receptive fields, is able to almost perfectly reconstruct stimulus locations within a low-dimensional representation. In contrast, a population of AIT neurons, despite each cell being spatially selective, provide less accurate low-dimensional reconstructions of stimulus locations. They produce instead only a topologically (categorically) correct rendition of space, which nevertheless might be critical for object and scene recognition. Furthermore, we found that the spatial representation recovered from population activity shows greater translation invariance in LIP than in AIT. We suggest that LIP spatial representations may be dimensionally isomorphic with 3D physical space, while in AIT spatial representations may reflect a more categorical representation of space (e.g., “next to” or “above”). PMID:21344010

Mosaic and Concerted Evolution in the Visual System of Birds

PubMed Central

Gutiérrez-Ibáñez, Cristián; Iwaniuk, Andrew N.; Moore, Bret A.; Fernández-Juricic, Esteban; Corfield, Jeremy R.; Krilow, Justin M.; Kolominsky, Jeffrey; Wylie, Douglas R.

2014-01-01

Two main models have been proposed to explain how the relative size of neural structures varies through evolution. In the mosaic evolution model, individual brain structures vary in size independently of each other, whereas in the concerted evolution model developmental constraints result in different parts of the brain varying in size in a coordinated manner. Several studies have shown variation of the relative size of individual nuclei in the vertebrate brain, but it is currently not known if nuclei belonging to the same functional pathway vary independently of each other or in a concerted manner. The visual system of birds offers an ideal opportunity to specifically test which of the two models apply to an entire sensory pathway. Here, we examine the relative size of 9 different visual nuclei across 98 species of birds. This includes data on interspecific variation in the cytoarchitecture and relative size of the isthmal nuclei, which has not been previously reported. We also use a combination of statistical analyses, phylogenetically corrected principal component analysis and evolutionary rates of change on the absolute and relative size of the nine nuclei, to test if visual nuclei evolved in a concerted or mosaic manner. Our results strongly indicate a combination of mosaic and concerted evolution (in the relative size of nine nuclei) within the avian visual system. Specifically, the relative size of the isthmal nuclei and parts of the tectofugal pathway covary across species in a concerted fashion, whereas the relative volume of the other visual nuclei measured vary independently of one another, such as that predicted by the mosaic model. Our results suggest the covariation of different neural structures depends not only on the functional connectivity of each nucleus, but also on the diversity of afferents and efferents of each nucleus. PMID:24621573

Cross-modal links among vision, audition, and touch in complex environments.

PubMed

Ferris, Thomas K; Sarter, Nadine B

2008-02-01

This study sought to determine whether performance effects of cross-modal spatial links that were observed in earlier laboratory studies scale to more complex environments and need to be considered in multimodal interface design. It also revisits the unresolved issue of cross-modal cuing asymmetries. Previous laboratory studies employing simple cues, tasks, and/or targets have demonstrated that the efficiency of processing visual, auditory, and tactile stimuli is affected by the modality, lateralization, and timing of surrounding cues. Very few studies have investigated these cross-modal constraints in the context of more complex environments to determine whether they scale and how complexity affects the nature of cross-modal cuing asymmetries. Amicroworld simulation of battlefield operations with a complex task set and meaningful visual, auditory, and tactile stimuli was used to investigate cuing effects for all cross-modal pairings. Significant asymmetric performance effects of cross-modal spatial links were observed. Auditory cues shortened response latencies for collocated visual targets but visual cues did not do the same for collocated auditory targets. Responses to contralateral (rather than ipsilateral) targets were faster for tactually cued auditory targets and each visual-tactile cue-target combination, suggesting an inhibition-of-return effect. The spatial relationships between multimodal cues and targets significantly affect target response times in complex environments. The performance effects of cross-modal links and the observed cross-modal cuing asymmetries need to be examined in more detail and considered in future interface design. The findings from this study have implications for the design of multimodal and adaptive interfaces and for supporting attention management in complex, data-rich domains.

Stimulus Dependency of Object-Evoked Responses in Human Visual Cortex: An Inverse Problem for Category Specificity

PubMed Central

Graewe, Britta; De Weerd, Peter; Farivar, Reza; Castelo-Branco, Miguel

2012-01-01

Many studies have linked the processing of different object categories to specific event-related potentials (ERPs) such as the face-specific N170. Despite reports showing that object-related ERPs are influenced by visual stimulus features, there is consensus that these components primarily reflect categorical aspects of the stimuli. Here, we re-investigated this idea by systematically measuring the effects of visual feature manipulations on ERP responses elicited by both structure-from-motion (SFM)-defined and luminance-defined object stimuli. SFM objects elicited a novel component at 200–250 ms (N250) over parietal and posterior temporal sites. We found, however, that the N250 amplitude was unaffected by restructuring SFM stimuli into meaningless objects based on identical visual cues. This suggests that this N250 peak was not uniquely linked to categorical aspects of the objects, but is strongly determined by visual stimulus features. We provide strong support for this hypothesis by parametrically manipulating the depth range of both SFM- and luminance-defined object stimuli and showing that the N250 evoked by SFM stimuli as well as the well-known N170 to static faces were sensitive to this manipulation. Importantly, this effect could not be attributed to compromised object categorization in low depth stimuli, confirming a strong impact of visual stimulus features on object-related ERP signals. As ERP components linked with visual categorical object perception are likely determined by multiple stimulus features, this creates an interesting inverse problem when deriving specific perceptual processes from variations in ERP components. PMID:22363479

Stimulus dependency of object-evoked responses in human visual cortex: an inverse problem for category specificity.

PubMed

Graewe, Britta; De Weerd, Peter; Farivar, Reza; Castelo-Branco, Miguel

2012-01-01

Many studies have linked the processing of different object categories to specific event-related potentials (ERPs) such as the face-specific N170. Despite reports showing that object-related ERPs are influenced by visual stimulus features, there is consensus that these components primarily reflect categorical aspects of the stimuli. Here, we re-investigated this idea by systematically measuring the effects of visual feature manipulations on ERP responses elicited by both structure-from-motion (SFM)-defined and luminance-defined object stimuli. SFM objects elicited a novel component at 200-250 ms (N250) over parietal and posterior temporal sites. We found, however, that the N250 amplitude was unaffected by restructuring SFM stimuli into meaningless objects based on identical visual cues. This suggests that this N250 peak was not uniquely linked to categorical aspects of the objects, but is strongly determined by visual stimulus features. We provide strong support for this hypothesis by parametrically manipulating the depth range of both SFM- and luminance-defined object stimuli and showing that the N250 evoked by SFM stimuli as well as the well-known N170 to static faces were sensitive to this manipulation. Importantly, this effect could not be attributed to compromised object categorization in low depth stimuli, confirming a strong impact of visual stimulus features on object-related ERP signals. As ERP components linked with visual categorical object perception are likely determined by multiple stimulus features, this creates an interesting inverse problem when deriving specific perceptual processes from variations in ERP components.

KEGGParser: parsing and editing KEGG pathway maps in Matlab.

PubMed

Arakelyan, Arsen; Nersisyan, Lilit

2013-02-15

KEGG pathway database is a collection of manually drawn pathway maps accompanied with KGML format files intended for use in automatic analysis. KGML files, however, do not contain the required information for complete reproduction of all the events indicated in the static image of a pathway map. Several parsers and editors of KEGG pathways exist for processing KGML files. We introduce KEGGParser-a MATLAB based tool for KEGG pathway parsing, semiautomatic fixing, editing, visualization and analysis in MATLAB environment. It also works with Scilab. The source code is available at http://www.mathworks.com/matlabcentral/fileexchange/37561.

Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex

PubMed Central

Coppola, David; White, Leonard E.; Wolf, Fred

2015-01-01

The architecture of iso-orientation domains in the primary visual cortex (V1) of placental carnivores and primates apparently follows species invariant quantitative laws. Dynamical optimization models assuming that neurons coordinate their stimulus preferences throughout cortical circuits linking millions of cells specifically predict these invariants. This might indicate that V1’s intrinsic connectome and its functional architecture adhere to a single optimization principle with high precision and robustness. To validate this hypothesis, it is critical to closely examine the quantitative predictions of alternative candidate theories. Random feedforward wiring within the retino-cortical pathway represents a conceptually appealing alternative to dynamical circuit optimization because random dimension-expanding projections are believed to generically exhibit computationally favorable properties for stimulus representations. Here, we ask whether the quantitative invariants of V1 architecture can be explained as a generic emergent property of random wiring. We generalize and examine the stochastic wiring model proposed by Ringach and coworkers, in which iso-orientation domains in the visual cortex arise through random feedforward connections between semi-regular mosaics of retinal ganglion cells (RGCs) and visual cortical neurons. We derive closed-form expressions for cortical receptive fields and domain layouts predicted by the model for perfectly hexagonal RGC mosaics. Including spatial disorder in the RGC positions considerably changes the domain layout properties as a function of disorder parameters such as position scatter and its correlations across the retina. However, independent of parameter choice, we find that the model predictions substantially deviate from the layout laws of iso-orientation domains observed experimentally. Considering random wiring with the currently most realistic model of RGC mosaic layouts, a pairwise interacting point process, the predicted layouts remain distinct from experimental observations and resemble Gaussian random fields. We conclude that V1 layout invariants are specific quantitative signatures of visual cortical optimization, which cannot be explained by generic random feedforward-wiring models. PMID:26575467

Joint brain connectivity estimation from diffusion and functional MRI data

NASA Astrophysics Data System (ADS)

Chu, Shu-Hsien; Lenglet, Christophe; Parhi, Keshab K.

2015-03-01

Estimating brain wiring patterns is critical to better understand the brain organization and function. Anatomical brain connectivity models axonal pathways, while the functional brain connectivity characterizes the statistical dependencies and correlation between the activities of various brain regions. The synchronization of brain activity can be inferred through the variation of blood-oxygen-level dependent (BOLD) signal from functional MRI (fMRI) and the neural connections can be estimated using tractography from diffusion MRI (dMRI). Functional connections between brain regions are supported by anatomical connections, and the synchronization of brain activities arises through sharing of information in the form of electro-chemical signals on axon pathways. Jointly modeling fMRI and dMRI data may improve the accuracy in constructing anatomical connectivity as well as functional connectivity. Such an approach may lead to novel multimodal biomarkers potentially able to better capture functional and anatomical connectivity variations. We present a novel brain network model which jointly models the dMRI and fMRI data to improve the anatomical connectivity estimation and extract the anatomical subnetworks associated with specific functional modes by constraining the anatomical connections as structural supports to the functional connections. The key idea is similar to a multi-commodity flow optimization problem that minimizes the cost or maximizes the efficiency for flow configuration and simultaneously fulfills the supply-demand constraint for each commodity. In the proposed network, the nodes represent the grey matter (GM) regions providing brain functionality, and the links represent white matter (WM) fiber bundles connecting those regions and delivering information. The commodities can be thought of as the information corresponding to brain activity patterns as obtained for instance by independent component analysis (ICA) of fMRI data. The concept of information flow is introduced and used to model the propagation of information between GM areas through WM fiber bundles. The link capacity, i.e., ability to transfer information, is characterized by the relative strength of fiber bundles, e.g., fiber count gathered from the tractography of dMRI data. The node information demand is considered to be proportional to the correlation between neural activity at various cortical areas involved in a particular functional mode (e.g. visual, motor, etc.). These two properties lead to the link capacity and node demand constraints in the proposed model. Moreover, the information flow of a link cannot exceed the demand from either end node. This is captured by the feasibility constraints. Two different cost functions are considered in the optimization formulation in this paper. The first cost function, the reciprocal of fiber strength represents the unit cost for information passing through the link. In the second cost function, a min-max (minimizing the maximal link load) approach is used to balance the usage of each link. Optimizing the first cost function selects the pathway with strongest fiber strength for information propagation. In the second case, the optimization procedure finds all the possible propagation pathways and allocates the flow proportionally to their strength. Additionally, a penalty term is incorporated with both the cost functions to capture the possible missing and weak anatomical connections. With this set of constraints and the proposed cost functions, solving the network optimization problem recovers missing and weak anatomical connections supported by the functional information and provides the functional-associated anatomical subnetworks. Feasibility is demonstrated using realistic diffusion and functional MRI phantom data. It is shown that the proposed model recovers the maximum number of true connections, with fewest number of false connections when compared with the connectivity derived from a joint probabilistic model using the expectation-maximization (EM) algorithm presented in a prior work. We also apply the proposed method to data provided by the Human Connectome Project (HCP).

The role of pulvinar in the transmission of information in the visual hierarchy.

PubMed

Cortes, Nelson; van Vreeswijk, Carl

2012-01-01

VISUAL RECEPTIVE FIELD (RF) ATTRIBUTES IN VISUAL CORTEX OF PRIMATES HAVE BEEN EXPLAINED MAINLY FROM CORTICAL CONNECTIONS: visual RFs progress from simple to complex through cortico-cortical pathways from lower to higher levels in the visual hierarchy. This feedforward flow of information is paired with top-down processes through the feedback pathway. Although the hierarchical organization explains the spatial properties of RFs, is unclear how a non-linear transmission of activity through the visual hierarchy can yield smooth contrast response functions in all level of the hierarchy. Depending on the gain, non-linear transfer functions create either a bimodal response to contrast, or no contrast dependence of the response in the highest level of the hierarchy. One possible mechanism to regulate this transmission of visual contrast information from low to high level involves an external component that shortcuts the flow of information through the hierarchy. A candidate for this shortcut is the Pulvinar nucleus of the thalamus. To investigate representation of stimulus contrast a hierarchical model network of ten cortical areas is examined. In each level of the network, the activity from the previous layer is integrated and then non-linearly transmitted to the next level. The arrangement of interactions creates a gradient from simple to complex RFs of increasing size as one moves from lower to higher cortical levels. The visual input is modeled as a Gaussian random input, whose width codes for the contrast. This input is applied to the first area. The output activity ratio among different contrast values is analyzed for the last level to observe sensitivity to a contrast and contrast invariant tuning. For a purely cortical system, the output of the last area can be approximately contrast invariant, but the sensitivity to contrast is poor. To account for an alternative visual processing pathway, non-reciprocal connections from and to a parallel pulvinar like structure of nine areas is coupled to the system. Compared to the pure feedforward model, cortico-pulvino-cortical output presents much more sensitivity to contrast and has a similar level of contrast invariance of the tuning.

The Role of Pulvinar in the Transmission of Information in the Visual Hierarchy

PubMed Central

Cortes, Nelson; van Vreeswijk, Carl

2012-01-01

Visual receptive field (RF) attributes in visual cortex of primates have been explained mainly from cortical connections: visual RFs progress from simple to complex through cortico-cortical pathways from lower to higher levels in the visual hierarchy. This feedforward flow of information is paired with top-down processes through the feedback pathway. Although the hierarchical organization explains the spatial properties of RFs, is unclear how a non-linear transmission of activity through the visual hierarchy can yield smooth contrast response functions in all level of the hierarchy. Depending on the gain, non-linear transfer functions create either a bimodal response to contrast, or no contrast dependence of the response in the highest level of the hierarchy. One possible mechanism to regulate this transmission of visual contrast information from low to high level involves an external component that shortcuts the flow of information through the hierarchy. A candidate for this shortcut is the Pulvinar nucleus of the thalamus. To investigate representation of stimulus contrast a hierarchical model network of ten cortical areas is examined. In each level of the network, the activity from the previous layer is integrated and then non-linearly transmitted to the next level. The arrangement of interactions creates a gradient from simple to complex RFs of increasing size as one moves from lower to higher cortical levels. The visual input is modeled as a Gaussian random input, whose width codes for the contrast. This input is applied to the first area. The output activity ratio among different contrast values is analyzed for the last level to observe sensitivity to a contrast and contrast invariant tuning. For a purely cortical system, the output of the last area can be approximately contrast invariant, but the sensitivity to contrast is poor. To account for an alternative visual processing pathway, non-reciprocal connections from and to a parallel pulvinar like structure of nine areas is coupled to the system. Compared to the pure feedforward model, cortico-pulvino-cortical output presents much more sensitivity to contrast and has a similar level of contrast invariance of the tuning. PMID:22654750

Visual field defects after missile injuries to the geniculo-striate pathway in man.

NASA Technical Reports Server (NTRS)

Koerner, F.; Teuber, H.-L.

1973-01-01

The main objective of the survey reported was a quantitative comparison of different visual functions at identical retinal points of individual patients. The possibility to develop objective forms of visual-field testing was also explored, taking into account reports by Frydrychowicz and Harms (1940) and Harms (1951). These investigators had insisted that pupillary responses to light are depressed in areas of homonymous scotomata. The shapes of homonymous visual field defects are discussed together with questions regarding the association and dissociation of symptoms.

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

DOE PAGES

King, Zachary A.; Lu, Justin; Drager, Andreas; ...

2015-10-17

In this study, genome-scale metabolic models are mathematically structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scalemore » metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.« less

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

PubMed Central

King, Zachary A.; Lu, Justin; Dräger, Andreas; Miller, Philip; Federowicz, Stephen; Lerman, Joshua A.; Ebrahim, Ali; Palsson, Bernhard O.; Lewis, Nathan E.

2016-01-01

Genome-scale metabolic models are mathematically-structured knowledge bases that can be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can generate and test hypotheses when integrated with experimental data. To maximize the value of these models, centralized repositories of high-quality models must be established, models must adhere to established standards and model components must be linked to relevant databases. Tools for model visualization further enhance their utility. To meet these needs, we present BiGG Models (http://bigg.ucsd.edu), a completely redesigned Biochemical, Genetic and Genomic knowledge base. BiGG Models contains more than 75 high-quality, manually-curated genome-scale metabolic models. On the website, users can browse, search and visualize models. BiGG Models connects genome-scale models to genome annotations and external databases. Reaction and metabolite identifiers have been standardized across models to conform to community standards and enable rapid comparison across models. Furthermore, BiGG Models provides a comprehensive application programming interface for accessing BiGG Models with modeling and analysis tools. As a resource for highly curated, standardized and accessible models of metabolism, BiGG Models will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data. PMID:26476456

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

PubMed Central

Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K.; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C.; Hoeng, Julia

2015-01-01

With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com PMID:25887162

Visualizing redox orbitals and their potentials in advanced lithium-ion battery materials using high-resolution x-ray Compton scattering

DOE PAGES

Hafiz, Hasnain; Suzuki, Kosuke; Barbiellini, Bernardo; ...

2017-08-02

Reduction-oxidation (redox) reactions are the key processes that underlie the batteries powering smartphones, laptops, and electric cars. A redox process involves transfer of electrons between two species. For example, in a lithium-ion battery, current is generated when conduction electrons from the lithium anode are transferred to the redox orbitals of the cathode material. The ability to visualize or image the redox orbitals and how these orbitals evolve under lithiation and delithiation processes is thus of great fundamental and practical interest for understanding the workings of battery materials. In this study, we show that inelastic scattering spectroscopy using high-energy x-ray photonsmore » (Compton scattering) can yield faithful momentum space images of the redox orbitals by considering lithium iron phosphate (LiFePO 4 or LFP) as an exemplar cathode battery material. Our analysis reveals a new link between voltage and the localization of transition metal 3d orbitals and provides insight into the puzzling mechanism of potential shift and how it is connected to the modification of the bond between the transition metal and oxygen atoms. Our study thus opens a novel spectroscopic pathway for improving the performance of battery materials.« less

Visualizing redox orbitals and their potentials in advanced lithium-ion battery materials using high-resolution x-ray Compton scattering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hafiz, Hasnain; Suzuki, Kosuke; Barbiellini, Bernardo

Reduction-oxidation (redox) reactions are the key processes that underlie the batteries powering smartphones, laptops, and electric cars. A redox process involves transfer of electrons between two species. For example, in a lithium-ion battery, current is generated when conduction electrons from the lithium anode are transferred to the redox orbitals of the cathode material. The ability to visualize or image the redox orbitals and how these orbitals evolve under lithiation and delithiation processes is thus of great fundamental and practical interest for understanding the workings of battery materials. In this study, we show that inelastic scattering spectroscopy using high-energy x-ray photonsmore » (Compton scattering) can yield faithful momentum space images of the redox orbitals by considering lithium iron phosphate (LiFePO 4 or LFP) as an exemplar cathode battery material. Our analysis reveals a new link between voltage and the localization of transition metal 3d orbitals and provides insight into the puzzling mechanism of potential shift and how it is connected to the modification of the bond between the transition metal and oxygen atoms. Our study thus opens a novel spectroscopic pathway for improving the performance of battery materials.« less

Awareness Becomes Necessary Between Adaptive Pattern Coding of Open and Closed Curvatures

PubMed Central

Sweeny, Timothy D.; Grabowecky, Marcia; Suzuki, Satoru

2012-01-01

Visual pattern processing becomes increasingly complex along the ventral pathway, from the low-level coding of local orientation in the primary visual cortex to the high-level coding of face identity in temporal visual areas. Previous research using pattern aftereffects as a psychophysical tool to measure activation of adaptive feature coding has suggested that awareness is relatively unimportant for the coding of orientation, but awareness is crucial for the coding of face identity. We investigated where along the ventral visual pathway awareness becomes crucial for pattern coding. Monoptic masking, which interferes with neural spiking activity in low-level processing while preserving awareness of the adaptor, eliminated open-curvature aftereffects but preserved closed-curvature aftereffects. In contrast, dichoptic masking, which spares spiking activity in low-level processing while wiping out awareness, preserved open-curvature aftereffects but eliminated closed-curvature aftereffects. This double dissociation suggests that adaptive coding of open and closed curvatures straddles the divide between weakly and strongly awareness-dependent pattern coding. PMID:21690314

Audiovisual Association Learning in the Absence of Primary Visual Cortex.

PubMed

Seirafi, Mehrdad; De Weerd, Peter; Pegna, Alan J; de Gelder, Beatrice

2015-01-01

Learning audiovisual associations is mediated by the primary cortical areas; however, recent animal studies suggest that such learning can take place even in the absence of the primary visual cortex. Other studies have demonstrated the involvement of extra-geniculate pathways and especially the superior colliculus (SC) in audiovisual association learning. Here, we investigated such learning in a rare human patient with complete loss of the bilateral striate cortex. We carried out an implicit audiovisual association learning task with two different colors of red and purple (the latter color known to minimally activate the extra-genicular pathway). Interestingly, the patient learned the association between an auditory cue and a visual stimulus only when the unseen visual stimulus was red, but not when it was purple. The current study presents the first evidence showing the possibility of audiovisual association learning in humans with lesioned striate cortex. Furthermore, in line with animal studies, it supports an important role for the SC in audiovisual associative learning.

FoxP2 is a Parvocellular-Specific Transcription Factor in the Visual Thalamus of Monkeys and Ferrets

PubMed Central

Iwai, Lena; Ohashi, Yohei; van der List, Deborah; Usrey, William Martin; Miyashita, Yasushi; Kawasaki, Hiroshi

2013-01-01

Although the parallel visual pathways are a fundamental basis of visual processing, our knowledge of their molecular properties is still limited. Here, we uncovered a parvocellular-specific molecule in the dorsal lateral geniculate nucleus (dLGN) of higher mammals. We found that FoxP2 transcription factor was specifically expressed in X cells of the adult ferret dLGN. Interestingly, FoxP2 was also specifically expressed in parvocellular layers 3–6 of the dLGN of adult old world monkeys, providing new evidence for a homology between X cells in the ferret dLGN and parvocellular cells in the monkey dLGN. Furthermore, this expression pattern was established as early as gestation day 140 in the embryonic monkey dLGN, suggesting that parvocellular specification has already occurred when the cytoarchitectonic dLGN layers are formed. Our results should help in gaining a fundamental understanding of the development, evolution, and function of the parallel visual pathways, which are especially prominent in higher mammals. PMID:22791804

A long-distance fluid transport pathway within fibrous connective tissues in patients with ankle edema.

PubMed

Li, Hongyi; Yang, Chongqing; Lu, Kuiyuan; Zhang, Liyang; Yang, Jiefu; Wang, Fang; Liu, Dongge; Cui, Di; Sun, Mingjun; Pang, Jianxin; Dai, Luru; Han, Dong; Liao, Fulong

2016-10-05

Although the microcirculatory dysfunctions of edema formation are well documented, the draining pattern of dermal edema lacks information. This study was to assess the potential drainage pathways of the interstitial fluid in patients with ankle edema using the anatomical and histological methods. Four amputees of lower leg participated in this study. Fluorescent imaging agent was injected into lateral ankle dermis in one volunteered patient before the amputation and three lower legs after the amputation. Physiologically in the volunteer or enhanced by cyclical compression on three amputated limbs, several fluorescent longitudinal pathways from ankle dermis to the broken end of the amputated legs were subsequently visualized and studied using histological methods, laser confocal microscopy and electron microscopy methods respectively. Interestingly, the fluorescent pathways confirmed to be fibrous connective tissues and the presence of two types: those of the cutaneous pathway (located in dermis or the interlobular septum among adipose tissues within the hypodermis) and those of the perivascular pathway (located in connective tissues surrounding the veins and the arteries). The intrinsic three-dimensional architecture of each fluorescent pathway was the longitudinally running and interconnected fibril bundles, upon which, an interfacial transport pathway within connective tissues was visualized by fluorescein. The current anatomical data suggested that a unique long-distance transport pathway composed of oriented fibrous connective tissues might play a pathophysiological role in draining dermal edema besides vascular circulations and provide novel understandings of general fibrous connective tissues in life science.

A New Method of Providing Communities With High-Resolution Maps of Present and Future Inundation Pathways: Two Examples From Massachusetts

NASA Astrophysics Data System (ADS)

Borrelli, M.; Mague, S. T.; Smith, T. L.

2015-12-01

A new method of mapping storm-tide (inundation) pathways and linking those data with tidal elevations in real-time for local managers is being developed. Separate, ongoing studies in two coastal towns in Massachusetts have demonstrated the strengths of this method. High-resolution lidar datasets are imported into 3D data visualization software and water levels are raised incrementally from the highest spring tide of the year to the storm of record +1 m. This range was identified to include 'nuisance flooding' as well as present and future inundation pathways not yet observed by local authorities caused by storms superimposed on projected sea level rise. Potential storm-tide pathways are identified using Lidar data but are then verified with extensive fieldwork using RTK-GPS instruments (tested vertical accuracy of 4.9 cm at 95%) to overcome the vertical uncertainty associated with Lidar data. The fieldwork serves two purposes, first is to field check the lidar data with the highest resolution instrument available and, second to verify and document the presence or absence of a storm-tide pathway. Having developed the map of storm tide pathways within a GIS environment referenced to a geodetic datum (NAVD88), a tide gauge or staff is installed in the town's harbor or other sheltered coastal area and the elevations of all storm tide pathways are then referenced to the local tidal datum. The benefit here is three-fold. First, local officials can use the high-resolution data set that is tied to a local tidal datum to autonomously monitor predicted storm surges and be prepared for inundation at sites prior to flooding. Second, storm-tide pathways that have heretofore never been inundated can be identified and steps can be taken to remove or minimize flooding hazards. Finally, identification of present and future storm tide pathways can be used to prioritize and budget proactive solutions in response to increases in chronic, nuisance and more frequent flooding associated with sea level rise and climate change. This method does not rely on costly numerical models that are often too coarsely gridded to be of use on a street-by-street basis. Lidar data are publicly available in many coastal areas and can be used with little training to new or already existing local or regional GIS staff.

Metabotropic glutamate receptor 5 shows different patterns of localization within the parallel visual pathways in macaque and squirrel monkeys.

PubMed

Shostak, Yuri; Wenger, Ashley; Mavity-Hudson, Julia; Casagrande, Vivien A

2014-09-24

Glutamate is used as an excitatory neurotransmitter by the koniocellular (K), magnocellular (M), and parvocellular (P) pathways to transfer signals from the primate lateral geniculate nucleus (LGN) to primary visual cortex (V1). Glutamate acts through both fast ionotropic receptors, which appear to carry the main sensory message, and slower, modulatory metabotropic receptors (mGluRs). In this study, we asked whether mGluR5 relates in distinct ways to the K, M, and P LGN axons in V1. To answer this question, we used light microscopic immunocytochemistry and preembedding electron microscopic immunogold labeling to determine the localization of mGluR5 within the layers of V1 in relation to the K, M, and P pathways in macaque and squirrel monkeys. These pathways were labeled separately via wheat germ agglutinin-horseradish peroxidase (WGA-HRP) injections targeting the LGN layers. mGluR5 is of interest because it: 1) has been shown to be expressed in the thalamic input layers; 2) appears to be responsible for some types of oscillatory firing, which could be important in the binding of visual features; and 3) has been associated with a number of sensory-motor gating-related pathologies, including schizophrenia and autism. Our results demonstrated the presence of mGluR5 in the neuropil of all V1 layers. This protein was lowest in IVCα (M input) and the infragranular layers. In layer IVC, mGluR5 also was found postsynaptic to about 30% of labeled axons, but the distribution was uneven, such that postsynaptic mGluR5 label tended to occur opposite smaller (presumed P), and not larger (presumed M) axon terminals. Only in the K pathway in layer IIIB, however, was mGluR5 always found in the axon terminals themselves. The presence of mGluR5 in K axons and not in M and P axons, and the presence of mGluR5 postsynaptic mainly to smaller P and not larger M axons suggest that the response to the release of glutamate is modulated in distinct ways within and between the parallel visual pathways of primates.

Automated retinofugal visual pathway reconstruction with multi-shell HARDI and FOD-based analysis.

PubMed

Kammen, Alexandra; Law, Meng; Tjan, Bosco S; Toga, Arthur W; Shi, Yonggang

2016-01-15

Diffusion MRI tractography provides a non-invasive modality to examine the human retinofugal projection, which consists of the optic nerves, optic chiasm, optic tracts, the lateral geniculate nuclei (LGN) and the optic radiations. However, the pathway has several anatomic features that make it particularly challenging to study with tractography, including its location near blood vessels and bone-air interface at the base of the cerebrum, crossing fibers at the chiasm, somewhat-tortuous course around the temporal horn via Meyer's Loop, and multiple closely neighboring fiber bundles. To date, these unique complexities of the visual pathway have impeded the development of a robust and automated reconstruction method using tractography. To overcome these challenges, we develop a novel, fully automated system to reconstruct the retinofugal visual pathway from high-resolution diffusion imaging data. Using multi-shell, high angular resolution diffusion imaging (HARDI) data, we reconstruct precise fiber orientation distributions (FODs) with high order spherical harmonics (SPHARM) to resolve fiber crossings, which allows the tractography algorithm to successfully navigate the complicated anatomy surrounding the retinofugal pathway. We also develop automated algorithms for the identification of ROIs used for fiber bundle reconstruction. In particular, we develop a novel approach to extract the LGN region of interest (ROI) based on intrinsic shape analysis of a fiber bundle computed from a seed region at the optic chiasm to a target at the primary visual cortex. By combining automatically identified ROIs and FOD-based tractography, we obtain a fully automated system to compute the main components of the retinofugal pathway, including the optic tract and the optic radiation. We apply our method to the multi-shell HARDI data of 215 subjects from the Human Connectome Project (HCP). Through comparisons with post-mortem dissection measurements, we demonstrate the retinotopic organization of the optic radiation including a successful reconstruction of Meyer's loop. Then, using the reconstructed optic radiation bundle from the HCP cohort, we construct a probabilistic atlas and demonstrate its consistency with a post-mortem atlas. Finally, we generate a shape-based representation of the optic radiation for morphometry analysis. Copyright © 2015 Elsevier Inc. All rights reserved.

Semantics of the visual environment encoded in parahippocampal cortex

PubMed Central

Bonner, Michael F.; Price, Amy Rose; Peelle, Jonathan E.; Grossman, Murray

2016-01-01

Semantic representations capture the statistics of experience and store this information in memory. A fundamental component of this memory system is knowledge of the visual environment, including knowledge of objects and their associations. Visual semantic information underlies a range of behaviors, from perceptual categorization to cognitive processes such as language and reasoning. Here we examine the neuroanatomic system that encodes visual semantics. Across three experiments, we found converging evidence indicating that knowledge of verbally mediated visual concepts relies on information encoded in a region of the ventral-medial temporal lobe centered on parahippocampal cortex. In an fMRI study, this region was strongly engaged by the processing of concepts relying on visual knowledge but not by concepts relying on other sensory modalities. In a study of patients with the semantic variant of primary progressive aphasia (semantic dementia), atrophy that encompassed this region was associated with a specific impairment in verbally mediated visual semantic knowledge. Finally, in a structural study of healthy adults from the fMRI experiment, gray matter density in this region related to individual variability in the processing of visual concepts. The anatomic location of these findings aligns with recent work linking the ventral-medial temporal lobe with high-level visual representation, contextual associations, and reasoning through imagination. Together this work suggests a critical role for parahippocampal cortex in linking the visual environment with knowledge systems in the human brain. PMID:26679216

Semantics of the Visual Environment Encoded in Parahippocampal Cortex.

PubMed

Bonner, Michael F; Price, Amy Rose; Peelle, Jonathan E; Grossman, Murray

2016-03-01

Semantic representations capture the statistics of experience and store this information in memory. A fundamental component of this memory system is knowledge of the visual environment, including knowledge of objects and their associations. Visual semantic information underlies a range of behaviors, from perceptual categorization to cognitive processes such as language and reasoning. Here we examine the neuroanatomic system that encodes visual semantics. Across three experiments, we found converging evidence indicating that knowledge of verbally mediated visual concepts relies on information encoded in a region of the ventral-medial temporal lobe centered on parahippocampal cortex. In an fMRI study, this region was strongly engaged by the processing of concepts relying on visual knowledge but not by concepts relying on other sensory modalities. In a study of patients with the semantic variant of primary progressive aphasia (semantic dementia), atrophy that encompassed this region was associated with a specific impairment in verbally mediated visual semantic knowledge. Finally, in a structural study of healthy adults from the fMRI experiment, gray matter density in this region related to individual variability in the processing of visual concepts. The anatomic location of these findings aligns with recent work linking the ventral-medial temporal lobe with high-level visual representation, contextual associations, and reasoning through imagination. Together, this work suggests a critical role for parahippocampal cortex in linking the visual environment with knowledge systems in the human brain.

Pathways for smiling, disgust and fear recognition in blindsight patients.

PubMed

Gerbella, Marzio; Caruana, Fausto; Rizzolatti, Giacomo

2017-08-31

The aim of the present review is to discuss the localization of circuits that allow recognition of emotional facial expressions in blindsight patients. Because recognition of facial expressions is function of different centers, and their localization is not always clear, we decided to discuss here three emotional facial expression - smiling, disgust, and fear - whose anatomical localization in the pregenual sector of the anterior cingulate cortex (pACC), anterior insula (AI), and amygdala, respectively, is well established. We examined, then, the possible pathways that may convey affective visual information to these centers following lesions of V1. We concluded that the pathway leading to pACC, AI, and amygdala involves the deep layers of the superior colliculus, the medial pulvinar, and the superior temporal sulcus region. We suggest that this visual pathway provides an image of the observed affective faces, which, although deteriorated, is sufficient to determine some overt behavior, but not to provide conscious experience of the presented stimuli. Copyright © 2017 Elsevier Ltd. All rights reserved.

Visual evoked potential assessment of the effects of glaucoma on visual subsystems.

PubMed

Greenstein, V C; Seliger, S; Zemon, V; Ritch, R

1998-06-01

The purpose of this study is to test the hypothesis that glaucoma leads to selective deficits in parallel pathways or channels. Sweep VEPs were obtained to isolated-check stimuli that were modulated sinusoidally in either isoluminant chromatic contrast or in positive and negative luminance contrast. Response functions were obtained from 14 control subjects, 15 patients with open-angle glaucoma, and seven glaucoma suspects. For all three groups of subjects we found characteristic differences between the VEP response functions to isoluminant chromatic contrast stimuli and to luminance contrast stimuli. The isoluminant chromatic stimulus conditions appeared to favor activity of the P-pathway, whereas the luminance contrast stimuli at low depths of modulation favored M-pathway activity. VEP responses for patients with OAG were significantly reduced for chromatic contrast and luminance contrast conditions, whereas VEP responses for glaucoma suspects were significantly reduced only for the 15-Hz positive luminance contrast condition. Our results suggest that both M- and P-pathways are affected by glaucoma.

OCT imaging of craniofacial anatomy in xenopus embryos (Conference Presentation)

NASA Astrophysics Data System (ADS)

Deniz, Engin; Jonas, Stephan M.; Griffin, John; Hooper, Michael C.; Choma, Michael A.; Khokha, Mustafa K.

2016-03-01

The etiology of craniofacial defects is incompletely understood. The ability to obtain large amounts of gene sequence data from families affected by craniofacial defects is opening up new ways to understand molecular genetic etiological factors. One important link between gene sequence data and clinical relevance is biological research into candidate genes and molecular pathways. We present our recent research using OCT as a nondestructive phenotyping modality of craniofacial morphology in Xenopus embryos, an important animal model for biological research in gene and pathway discovery. We define 2D and 3D scanning protocols for a standardized approach to craniofacial imaging in Xenopus embryos. We define standard views and planar reconstructions for visualizing normal anatomy and landmarks. We compare these views and reconstructions to traditional histopathology using alcian blue staining. In addition to being 3D, nondestructive, and having much faster throughout, OCT can identify craniofacial features that are lost during traditional histopathological preparation. We also identify quantitative morphometric parameters to define normative craniofacial anatomy. We also note that craniofacial and cardiac defects are not infrequently present in the same patient (e.g velocardiofacial syndrome). Given that OCT excels at certain aspects of cardiac imaging in Xenopus embryos, our work highlights the potential of using OCT and Xenopus to study molecular genetic factors that impact both cardiac and craniofacial development.

The role of O-GlcNAc signaling in the pathogenesis of diabetic retinopathy.

PubMed

Semba, Richard D; Huang, Hu; Lutty, Gerard A; Van Eyk, Jennifer E; Hart, Gerald W

2014-04-01

Diabetic retinopathy is a leading cause of blindness worldwide. Despite laser and surgical treatments, antiangiogenic and other therapies, and strict metabolic control, many patients progress to visual impairment and blindness. New insights are needed into the pathophysiology of diabetic retinopathy in order to develop new methods to improve the detection and treatment of disease and the prevention of blindness. Hyperglycemia and diabetes result in increased flux through the hexosamine biosynthetic pathway, which, in turn, results in increased PTM of Ser/Thr residues of proteins by O-linked β-N-acetylglucosamine (O-GlcNAc). O-GlcNAcylation is involved in regulation of many nuclear and cytoplasmic proteins in a manner similar to protein phosphorylation. Altered O-GlcNAc signaling has been implicated in the pathogenesis of diabetes and may play an important role in the pathogenesis of diabetic retinopathy. The goal of this review is to summarize the biology of the hexosamine biosynthesis pathway and O-GlcNAc signaling, to present the current evidence for the role of O-GlcNAc signaling in diabetes and diabetic retinopathy, and to discuss future directions for research on O-GlcNAc in the pathogenesis of diabetic retinopathy. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Latanoprostene bunod ophthalmic solution 0.024% for IOP lowering in glaucoma and ocular hypertension.

PubMed

Kaufman, Paul L

2017-03-01

Intraocular pressure (IOP)-lowering has been demonstrated to slow the progression or onset of visual field loss in open-angle glaucoma (OAG) or ocular hypertension (OHT). Pharmacological lowering of IOP is the most common initial intervention in patients with OAG or OHT, however, many patients will require more than one therapy to achieve target IOP. Latanoprostene bunod is a novel nitric oxide (NO)-donating prostaglandin F2α analog for the reduction of IOP. Areas covered: Current knowledge concerning the mechanism of action of latanoprostene bunod is presented. Additionally, clinical safety and efficacy data from published Phase 1 (KRONUS), Phase 2 (VOYAGER, CONSTELLATION) and Phase 3 (APOLLO, LUNAR, JUPITER) studies are reviewed. Expert opinion: Latanoprostene bunod is a dual mechanism, dual pathway molecule, consisting of latanoprost acid, which is known to enhance uveoscleral (unconventional) outflow by upregulating matrix metalloproteinase expression and remodeling of the ciliary muscle's extracellular matrix, linked to an NO-donating moiety, which enhances trabecular meshwork/Schlemm's canal (conventional) outflow by inducing cytoskeletal relaxation via the soluble guanylyl cyclase-cyclic guanosine monophosphate (sGC-cGMP) signaling pathway. Latanoprostene bunod 0.024% solution applied topically once daily appears more effective in reducing IOP in OHT and OAG subjects than either latanoprost or timolol, with a side effect profile similar to that of latanoprost.

Object-processing neural efficiency differentiates object from spatial visualizers.

PubMed

Motes, Michael A; Malach, Rafael; Kozhevnikov, Maria

2008-11-19

The visual system processes object properties and spatial properties in distinct subsystems, and we hypothesized that this distinction might extend to individual differences in visual processing. We conducted a functional MRI study investigating the neural underpinnings of individual differences in object versus spatial visual processing. Nine participants of high object-processing ability ('object' visualizers) and eight participants of high spatial-processing ability ('spatial' visualizers) were scanned, while they performed an object-processing task. Object visualizers showed lower bilateral neural activity in lateral occipital complex and lower right-lateralized neural activity in dorsolateral prefrontal cortex. The data indicate that high object-processing ability is associated with more efficient use of visual-object resources, resulting in less neural activity in the object-processing pathway.

Investigation of visual fatigue/discomfort generated by S3D video using eye-tracking data

NASA Astrophysics Data System (ADS)

Iatsun, Iana; Larabi, Mohamed-Chaker; Fernandez-Maloigne, Christine

2013-03-01

Stereoscopic 3D is undoubtedly one of the most attractive content. It has been deployed intensively during the last decade through movies and games. Among the advantages of 3D are the strong involvement of viewers and the increased feeling of presence. However, the sanitary e ects that can be generated by 3D are still not precisely known. For example, visual fatigue and visual discomfort are among symptoms that an observer may feel. In this paper, we propose an investigation of visual fatigue generated by 3D video watching, with the help of eye-tracking. From one side, a questionnaire, with the most frequent symptoms linked with 3D, is used in order to measure their variation over time. From the other side, visual characteristics such as pupil diameter, eye movements ( xations and saccades) and eye blinking have been explored thanks to data provided by the eye-tracker. The statistical analysis showed an important link between blinking duration and number of saccades with visual fatigue while pupil diameter and xations are not precise enough and are highly dependent on content. Finally, time and content play an important role in the growth of visual fatigue due to 3D watching.

Recruitment of Occipital Cortex during Sensory Substitution Training Linked to Subjective Experience of Seeing in People with Blindness

PubMed Central

Ortiz, Tomás; Poch, Joaquín; Santos, Juan M.; Requena, Carmen; Martínez, Ana M.; Ortiz-Terán, Laura; Turrero, Agustín; Barcia, Juan; Nogales, Ramón; Calvo, Agustín; Martínez, José M.; Córdoba, José L.; Pascual-Leone, Alvaro

2011-01-01

Over three months of intensive training with a tactile stimulation device, 18 blind and 10 blindfolded seeing subjects improved in their ability to identify geometric figures by touch. Seven blind subjects spontaneously reported ‘visual qualia’, the subjective sensation of seeing flashes of light congruent with tactile stimuli. In the latter subjects tactile stimulation evoked activation of occipital cortex on electroencephalography (EEG). None of the blind subjects who failed to experience visual qualia, despite identical tactile stimulation training, showed EEG recruitment of occipital cortex. None of the blindfolded seeing humans reported visual-like sensations during tactile stimulation. These findings support the notion that the conscious experience of seeing is linked to the activation of occipital brain regions in people with blindness. Moreover, the findings indicate that provision of visual information can be achieved through non-visual sensory modalities which may help to minimize the disability of blind individuals, affording them some degree of object recognition and navigation aid. PMID:21853098

Link between orientation and retinotopic maps in primary visual cortex

PubMed Central

Paik, Se-Bum; Ringach, Dario L.

2012-01-01

Maps representing the preference of neurons for the location and orientation of a stimulus on the visual field are a hallmark of primary visual cortex. It is not yet known how these maps develop and what function they play in visual processing. One hypothesis postulates that orientation maps are initially seeded by the spatial interference of ON- and OFF-center retinal receptive field mosaics. Here we show that such a mechanism predicts a link between the layout of orientation preferences around singularities of different signs and the cardinal axes of the retinotopic map. Moreover, we confirm the predicted relationship holds in tree shrew primary visual cortex. These findings provide additional support for the notion that spatially structured input from the retina may provide a blueprint for the early development of cortical maps and receptive fields. More broadly, it raises the possibility that spatially structured input from the periphery may shape the organization of primary sensory cortex of other modalities as well. PMID:22509015

Multi-focus and multi-level techniques for visualization and analysis of networks with thematic data

NASA Astrophysics Data System (ADS)

Cossalter, Michele; Mengshoel, Ole J.; Selker, Ted

2013-01-01

Information-rich data sets bring several challenges in the areas of visualization and analysis, even when associated with node-link network visualizations. This paper presents an integration of multi-focus and multi-level techniques that enable interactive, multi-step comparisons in node-link networks. We describe NetEx, a visualization tool that enables users to simultaneously explore different parts of a network and its thematic data, such as time series or conditional probability tables. NetEx, implemented as a Cytoscape plug-in, has been applied to the analysis of electrical power networks, Bayesian networks, and the Enron e-mail repository. In this paper we briefly discuss visualization and analysis of the Enron social network, but focus on data from an electrical power network. Specifically, we demonstrate how NetEx supports the analytical task of electrical power system fault diagnosis. Results from a user study with 25 subjects suggest that NetEx enables more accurate isolation of complex faults compared to an especially designed software tool.

Sensitivity of visual evoked potentials and spectral domain optical coherence tomography in early relapsing remitting multiple sclerosis.

PubMed

Behbehani, Raed; Ahmed, Samar; Al-Hashel, Jasem; Rousseff, Rossen T; Alroughani, Raed

2017-02-01

Visual evoked potentials and spectral-domain optical coherence tomography are common ancillary studies that assess the visual pathways from a functional and structural aspect, respectively. To compare prevalence of abnormalities of Visual evoked potentials (VEP) and spectral-domain optical coherence tomography (SDOCT) in patients with relapsing remitting multiple sclerosis (RRMS). A cross-sectional study of 100 eyes with disease duration of less than 5 years since the diagnosis. Correlation between retinal nerve fiber layer and ganglion-cell/inner plexiform layer with pattern-reversal visual evoked potentials amplitude and latency and contrast sensitivity was performed. The prevalence of abnormalities in pattern-reversal visual VEP was 56% while that of SOCT was 48% in all eyes. There was significant negative correlations between the average RNFL (r=-0.34, p=0.001) and GCIPL (r=-0.39, p<0.001) with VEP latency. In eyes with prior optic neuritis, a significant negative correlation was seen between average RNFL (r=-0.33, p=0.037) and GCIPL (r=-0.40, p=0.010) with VEP latency. We have found higher prevalence of VEP abnormalities than SCOCT in early relapsing-remitting multiple sclerosis. This suggests that VEP has a higher sensitivity for detecting lesions of the visual pathway in patients with early RRMS. Copyright © 2016 Elsevier B.V. All rights reserved.

Similar prevalence and magnitude of auditory-evoked and visually evoked activity in the frontal eye fields: implications for multisensory motor control.

PubMed

Caruso, Valeria C; Pages, Daniel S; Sommer, Marc A; Groh, Jennifer M

2016-06-01

Saccadic eye movements can be elicited by more than one type of sensory stimulus. This implies substantial transformations of signals originating in different sense organs as they reach a common motor output pathway. In this study, we compared the prevalence and magnitude of auditory- and visually evoked activity in a structure implicated in oculomotor processing, the primate frontal eye fields (FEF). We recorded from 324 single neurons while 2 monkeys performed delayed saccades to visual or auditory targets. We found that 64% of FEF neurons were active on presentation of auditory targets and 87% were active during auditory-guided saccades, compared with 75 and 84% for visual targets and saccades. As saccade onset approached, the average level of population activity in the FEF became indistinguishable on visual and auditory trials. FEF activity was better correlated with the movement vector than with the target location for both modalities. In summary, the large proportion of auditory-responsive neurons in the FEF, the similarity between visual and auditory activity levels at the time of the saccade, and the strong correlation between the activity and the saccade vector suggest that auditory signals undergo tailoring to match roughly the strength of visual signals present in the FEF, facilitating accessing of a common motor output pathway. Copyright © 2016 the American Physiological Society.

Disturbed default mode network connectivity patterns in Alzheimer's disease associated with visual processing.

PubMed

Krajcovicova, Lenka; Mikl, Michal; Marecek, Radek; Rektorova, Irena

2014-01-01

Changes in connectivity of the posterior node of the default mode network (DMN) were studied when switching from baseline to a cognitive task using functional magnetic resonance imaging. In all, 15 patients with mild to moderate Alzheimer's disease (AD) and 18 age-, gender-, and education-matched healthy controls (HC) participated in the study. Psychophysiological interactions analysis was used to assess the specific alterations in the DMN connectivity (deactivation-based) due to psychological effects from the complex visual scene encoding task. In HC, we observed task-induced connectivity decreases between the posterior cingulate and middle temporal and occipital visual cortices. These findings imply successful involvement of the ventral visual pathway during the visual processing in our HC cohort. In AD, involvement of the areas engaged in the ventral visual pathway was observed only in a small volume of the right middle temporal gyrus. Additional connectivity changes (decreases) in AD were present between the posterior cingulate and superior temporal gyrus when switching from baseline to task condition. These changes are probably related to both disturbed visual processing and the DMN connectivity in AD and reflect deficits and compensatory mechanisms within the large scale brain networks in this patient population. Studying the DMN connectivity using psychophysiological interactions analysis may provide a sensitive tool for exploring early changes in AD and their dynamics during the disease progression.

Quantifying the Movement and Dissolution of Fugitive Methane in Shallow Aquifers: Visualization Experiments

NASA Astrophysics Data System (ADS)

Van De Ven, C. J. C.; Mumford, K. G.

2016-12-01

The environmental impact and potential human health implications, specifically from the contamination of groundwater sources, has sparked controversy around shale gas extraction in North America. It is clear that understanding the effects of hydraulic fracturing on shallow fresh water aquifers is of great importance, including the threat of stray gas (also referred to as fugitive methane) on groundwater quality. Faulty wells provide a preferential pathway for free gas phase (mostly methane) to migrate from deeper gas-bearing formations of natural gas to shallow aquifers, followed by its dissolution into the surrounding groundwater. An increased understanding of the fate of fugitive methane in shallow aquifers is required to assess the potential risks associated with current and future operations, as well as to better link gas migration, dissolution and the deterioration of groundwater quality. In this study, a series of laboratory experiments were performed using carbon dioxide (CO2) gas as a surrogate for methane to improve our understanding of gas dissolution in groundwater systems. Using CO2, a novel laboratory technique was developed that allows the measurement of dissolved CO2 concentrations using image analysis alongside visualization of free gas mobilization. The technique is based on the acidification of water during CO2 dissolution, which causes a colour change in an indicator dye. The colour change is recorded using a visual light transmission technique, in which digital images are used to track dissolved concentrations at high spatial (1 mm) and temporal (5 s) resolutions in a two-dimensional (25 × 25 × 1 cm3) flow cell. The experiments were completed in both homogeneous sand packs and sand packs containing layered heterogeneities to investigate the dissolution of both gas fingers and gas pools. The results demonstrate the potential of this novel technique for investigating gas dissolution, and showed significant tailing of dissolved CO2 and persistence of other gas phase components. This technique will aid in the development of conceptual models to link fugitive methane to groundwater contamination and provide detailed data required for the validation of numerical models that account for gas-water mass transfer; both of which are required for the development of sound monitoring techniques.

Thinner retinal layers are associated with changes in the visual pathway: A population-based study.

PubMed

Mutlu, Unal; Ikram, Mohammad K; Roshchupkin, Gennady V; Bonnemaijer, Pieter W M; Colijn, Johanna M; Vingerling, Johannes R; Niessen, Wiro J; Ikram, Mohammad A; Klaver, Caroline C W; Vernooij, Meike W

2018-06-23

Increasing evidence shows that thinner retinal nerve fiber layer (RNFL) and ganglion cell layer (GCL), assessed on optical coherence tomography (OCT), are reflecting global brain atrophy. Yet, little is known on the relation of these layers with specific brain regions. Using voxel-based analysis, we aimed to unravel specific brain regions associated with these retinal layers. We included 2,235 persons (mean age: 67.3 years, 55% women) from the Rotterdam Study (2007-2012) who had gradable retinal OCT images and brain magnetic resonance imaging (MRI) scans, including diffusion tensor (DT) imaging. Thicknesses of peripapillary RNFL and perimacular GCL were measured using an automated segmentation algorithm. Voxel-based morphometry protocols were applied to process DT-MRI data. We investigated the association between retinal layer thickness with voxel-wise gray matter density and white matter microstructure by performing linear regression models. We found that thinner RNFL and GCL were associated with lower gray matter density in the visual cortex, and with lower fractional anisotropy and higher mean diffusivity in white matter tracts that are part of the optic radiation. Furthermore, thinner GCL was associated with lower gray matter density of the thalamus. Thinner RNFL and GCL are associated with gray and white matter changes in the visual pathway suggesting that retinal thinning on OCT may be specifically associated with changes in the visual pathway rather than with changes in the global brain. These findings may serve as a basis for understanding visual symptoms in elderly patients, patients with Alzheimer's disease, or patients with posterior cortical atrophy. © 2018 Wiley Periodicals, Inc.

Effects of rivastigmine on visual attention in subjects with amnestic mild cognitive impairment: A serial functional MRI activation pilot-study.

PubMed

Bokde, Arun L W; Cavedo, Enrica; Lopez-Bayo, Patricia; Lista, Simone; Meindl, Thomas; Born, Christine; Galluzzi, Samantha; Faltraco, Frank; Dubois, Bruno; Teipel, Stefan J; Reiser, Maximilian; Möller, Hans-Jürgen; Hampel, Harald

2016-03-30

A pilot study to investigate the effects of rivastigmine on the brain activation pattern due to visual attention tasks in a group of amnestic Mild Cognitive Impaired patients (aMCI). The design was an initial three-month double blind period with a rivastigmine and placebo arms, followed by a nine-month open-label period. All patients underwent serial functional magnetic resonance imaging (fMRI) at baseline, and after three and six months of follow-up. Primary endpoint was the effect of rivastigmine on functional brain changes during visual attention (face and location matching) tasks. There were five in the rivastigmine arm and two in the placebo arm. The face matching task showed higher activation of visual areas after three months of treatment but no differences compared to baseline at six months. The location matching task showed a higher activation along the dorsal visual pathway at both three and six months follow ups. Treatment with rivastigmine demonstrates a significant effect on brain activation of the dorsal visual pathway during a location matching task in patients with aMCI. Our data support the potential use of task fMRI to map specific treatment effects of cholinergic drugs during prodromal stages of Alzheimer's disease (AD). Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Pharmacologic attenuation of cross-modal sensory augmentation within the chronic pain insula

PubMed Central

Harte, Steven E.; Ichesco, Eric; Hampson, Johnson P.; Peltier, Scott J.; Schmidt-Wilcke, Tobias; Clauw, Daniel J.; Harris, Richard E.

2016-01-01

Abstract Pain can be elicited through all mammalian sensory pathways yet cross-modal sensory integration, and its relationship to clinical pain, is largely unexplored. Centralized chronic pain conditions such as fibromyalgia are often associated with symptoms of multisensory hypersensitivity. In this study, female patients with fibromyalgia demonstrated cross-modal hypersensitivity to visual and pressure stimuli compared with age- and sex-matched healthy controls. Functional magnetic resonance imaging revealed that insular activity evoked by an aversive level of visual stimulation was associated with the intensity of fibromyalgia pain. Moreover, attenuation of this insular activity by the analgesic pregabalin was accompanied by concomitant reductions in clinical pain. A multivariate classification method using support vector machines (SVM) applied to visual-evoked brain activity distinguished patients with fibromyalgia from healthy controls with 82% accuracy. A separate SVM classification of treatment effects on visual-evoked activity reliably identified when patients were administered pregabalin as compared with placebo. Both SVM analyses identified significant weights within the insular cortex during aversive visual stimulation. These data suggest that abnormal integration of multisensory and pain pathways within the insula may represent a pathophysiological mechanism in some chronic pain conditions and that insular response to aversive visual stimulation may have utility as a marker for analgesic drug development. PMID:27101425

Multiple Pathways Linking Racism to Health Outcomes

PubMed Central

Harrell, Camara Jules P.; Burford, Tanisha I.; Cage, Brandi N.; Nelson, Travette McNair; Shearon, Sheronda; Thompson, Adrian; Green, Steven

2012-01-01

This commentary discusses advances in the conceptual understanding of racism and selected research findings in the social neurosciences. The traditional stress and coping model holds that racism constitutes a source of aversive experiences that, when perceived by the individual, eventually lead to poor health outcomes. Current evidence points to additional psychophysiological pathways linking facets of racist environments with physiological reactions that contribute to disease. The alternative pathways emphasize prenatal experiences, subcortical emotional neural circuits, conscious and preconscious emotion regulation, perseverative cognitions, and negative affective states stemming from racist cognitive schemata. Recognition of these pathways challenges change agents to use an array of cognitive and self-controlling interventions in mitigating racism’s impact. Additionally, it charges policy makers to develop strategies that eliminate deep-seated structural aspects of racism in society. PMID:22518195

Aggressive Marital Conflict, Maternal Harsh Punishment, and Child Aggressive-Disruptive Behavior: Evidence for Direct and Mediated Relations

PubMed Central

Erath, Stephen A.; Bierman, Karen L.

2009-01-01

Direct associations between aggressive marital conflict and child aggressive-disruptive behavior at home and school were explored in this cross-sectional study of 360 kindergarten children. In addition, mediated pathways linking aggressive marital conflict to maternal harsh punishment to child aggressive-disruptive behavior were examined. Moderation analyses explored how the overall frequency of marital disagreement might buffer or exacerbate the impact of aggressive marital conflict on maternal harsh punishment and child aggressive-disruptive behavior. Hierarchical regressions revealed direct pathways linking aggressive marital conflict to child aggressive-disruptive behavior at home and school and a partially mediated pathway linking aggressive marital conflict to child aggressive-disruptive behavior at home. Further analyses revealed that rates of marital disagreement moderated the association between aggressive marital conflict and child aggressive-disruptive behavior at home, with an attenuated association at high rates of marital disagreement as compared with low rates of marital disagreement. PMID:16756397

Childhood emotional abuse, negative emotion-driven impulsivity, and alcohol use in young adulthood☆

PubMed Central

Shin, Sunny H.; Lee, Sungkyu; Jeon, Sae-Mi; Wills, Thomas A.

2015-01-01

Childhood emotional abuse has been linked to problematic alcohol use in later life but there is a paucity of empirically based knowledge about the developmental pathways linking emotional abuse and alcohol use in young adulthood. Using a community sample of young individuals aged 18–25 (N = 268; female 52%), we performed structural equation modeling to investigate whether emotional abuse influences alcohol use through urgent personality trait and to determine pathways for these effects in a multivariate context. We also examined variations in these pathways by four different alcohol use outcomes including frequency of alcohol use, binge drinking, alcohol-related problems, and alcohol use disorders (AUD). The present study found that emotional abuse was related to urgency, which in turn influenced four types of alcohol use. Urgency may play a significant role in linking childhood maltreatment to alcohol use in young adulthood. PMID:25743371

Childhood emotional abuse, negative emotion-driven impulsivity, and alcohol use in young adulthood.

PubMed

Shin, Sunny H; Lee, Sungkyu; Jeon, Sae-Mi; Wills, Thomas A

2015-12-01

Childhood emotional abuse has been linked to problematic alcohol use in later life but there is a paucity of empirically based knowledge about the developmental pathways linking emotional abuse and alcohol use in young adulthood. Using a community sample of young individuals aged 18-25 (N=268; female 52%), we performed structural equation modeling to investigate whether emotional abuse influences alcohol use through urgent personality trait and to determine pathways for these effects in a multivariate context. We also examined variations in these pathways by four different alcohol use outcomes including frequency of alcohol use, binge drinking, alcohol-related problems, and alcohol use disorders (AUD). The present study found that emotional abuse was related to urgency, which in turn influenced four types of alcohol use. Urgency may play a significant role in linking childhood maltreatment to alcohol use in young adulthood. Copyright © 2015. Published by Elsevier Ltd.

Disentangling brain activity related to the processing of emotional visual information and emotional arousal.

PubMed

Kuniecki, Michał; Wołoszyn, Kinga; Domagalik, Aleksandra; Pilarczyk, Joanna

2018-05-01

Processing of emotional visual information engages cognitive functions and induces arousal. We aimed to examine the modulatory role of emotional valence on brain activations linked to the processing of visual information and those linked to arousal. Participants were scanned and their pupil size was measured while viewing negative and neutral images. The visual noise was added to the images in various proportions to parametrically manipulate the amount of visual information. Pupil size was used as an index of physiological arousal. We show that arousal induced by the negative images, as compared to the neutral ones, is primarily related to greater amygdala activity while increasing visibility of negative content to enhanced activity in the lateral occipital complex (LOC). We argue that more intense visual processing of negative scenes can occur irrespective of the level of arousal. It may suggest that higher areas of the visual stream are fine-tuned to process emotionally relevant objects. Both arousal and processing of emotional visual information modulated activity within the ventromedial prefrontal cortex (vmPFC). Overlapping activations within the vmPFC may reflect the integration of these aspects of emotional processing. Additionally, we show that emotionally-evoked pupil dilations are related to activations in the amygdala, vmPFC, and LOC.

Alpha-Band Rhythms in Visual Task Performance: Phase-Locking by Rhythmic Sensory Stimulation

PubMed Central

de Graaf, Tom A.; Gross, Joachim; Paterson, Gavin; Rusch, Tessa; Sack, Alexander T.; Thut, Gregor

2013-01-01

Oscillations are an important aspect of neuronal activity. Interestingly, oscillatory patterns are also observed in behaviour, such as in visual performance measures after the presentation of a brief sensory event in the visual or another modality. These oscillations in visual performance cycle at the typical frequencies of brain rhythms, suggesting that perception may be closely linked to brain oscillations. We here investigated this link for a prominent rhythm of the visual system (the alpha-rhythm, 8–12 Hz) by applying rhythmic visual stimulation at alpha-frequency (10.6 Hz), known to lead to a resonance response in visual areas, and testing its effects on subsequent visual target discrimination. Our data show that rhythmic visual stimulation at 10.6 Hz: 1) has specific behavioral consequences, relative to stimulation at control frequencies (3.9 Hz, 7.1 Hz, 14.2 Hz), and 2) leads to alpha-band oscillations in visual performance measures, that 3) correlate in precise frequency across individuals with resting alpha-rhythms recorded over parieto-occipital areas. The most parsimonious explanation for these three findings is entrainment (phase-locking) of ongoing perceptually relevant alpha-band brain oscillations by rhythmic sensory events. These findings are in line with occipital alpha-oscillations underlying periodicity in visual performance, and suggest that rhythmic stimulation at frequencies of intrinsic brain-rhythms can be used to reveal influences of these rhythms on task performance to study their functional roles. PMID:23555873

A longitudinal study of visual function in carriers of X-linked recessive retinitis pigmentosa.

PubMed

Grover, S; Fishman, G A; Anderson, R J; Lindeman, M

2000-02-01

This study was carried out to evaluate the progression of visual function impairment in carriers of X-linked recessive retinitis pigmentosa. We also assessed the relationship between the retinal findings at presentation and the extent of deterioration. Observational, retrospective, case series. Twenty-seven carriers of X-linked recessive retinitis pigmentosa. Each carrier was clinically categorized into one of four grades (grades 0 through 3) depending on the presence or absence of a tapetal-like retinal reflex and the extent of peripheral pigmentary degeneration. A complete ophthalmologic examination was performed and data for visual acuity, visual field area, and electroretinographic measurements were collected on the most recent visit in both eyes. These were then compared with similar data obtained on their initial visits. A comparison of visual function was carried out between the initial visit and the most recent visit on each carrier. The visual acuity was measured with Snellen's acuity charts. The visual fields to targets V-4-e and II-4-e were planimeterized and used for the analysis. The electroretinographic (ERG) measures used were light-adapted single-flash b-wave amplitudes and 30-Hz red flicker for cone function, dark-adapted maximal b-wave amplitudes, and response to a low intensity blue-flash for rod function. None of the 11 carriers with a tapetal-like reflex only (grade 1) showed any significant change in visual acuity or fields as compared with 3 of 7 (43%) carriers with diffuse peripheral pigmentary findings (grade 3) who showed significant deterioration in visual acuity in at least one eye, and 6 of 7 (86%) who showed a significant decrease in visual field area with at least one target size in at least one eye. By comparison, only 1 of 10 carriers with a grade 1 fundus finding demonstrated a significant decrease in maximal dark-adapted ERG function as compared with 5 of 6 (83%) carriers with grade 3 in response to a single-flash stimulus and with 4 of 5 (80%) carriers in response to a single-flash blue stimulus. For the single-flash photopic response, none of the 10 carriers with grade 1 showed any significant deterioration, whereas 2 of 4 (50%) with grade 3 did show such deterioration. The ERG responses for carriers with grade 2 were in between the extent of decrease in ERG amplitudes of those in carriers with grades 1 and 3. In our cohort of X-linked retinitis pigmentosa carriers, those with only a tapetal-like retinal reflex at presentation had a better prognosis to retain visual function than those with peripheral retinal pigmentation. These data are useful in counseling such carriers as to their visual prognosis.

Visual Evoked Cortical Potential (VECP) Elicited by Sinusoidal Gratings Controlled by Pseudo-Random Stimulation

PubMed Central

Araújo, Carolina S.; Souza, Givago S.; Gomes, Bruno D.; Silveira, Luiz Carlos L.

2013-01-01

The contributions of contrast detection mechanisms to the visual cortical evoked potential (VECP) have been investigated studying the contrast-response and spatial frequency-response functions. Previously, the use of m-sequences for stimulus control has been almost restricted to multifocal electrophysiology stimulation and, in some aspects, it substantially differs from conventional VECPs. Single stimulation with spatial contrast temporally controlled by m-sequences has not been extensively tested or compared to multifocal techniques. Our purpose was to evaluate the influence of spatial frequency and contrast of sinusoidal gratings on the VECP elicited by pseudo-random stimulation. Nine normal subjects were stimulated by achromatic sinusoidal gratings driven by pseudo random binary m-sequence at seven spatial frequencies (0.4–10 cpd) and three stimulus sizes (4°, 8°, and 16° of visual angle). At 8° subtence, six contrast levels were used (3.12–99%). The first order kernel (K1) did not provide a consistent measurable signal across spatial frequencies and contrasts that were tested–signal was very small or absent–while the second order kernel first (K2.1) and second (K2.2) slices exhibited reliable responses for the stimulus range. The main differences between results obtained with the K2.1 and K2.2 were in the contrast gain as measured in the amplitude versus contrast and amplitude versus spatial frequency functions. The results indicated that K2.1 was dominated by M-pathway, but for some stimulus condition some P-pathway contribution could be found, while the second slice reflected the P-pathway contribution. The present work extended previous findings of the visual pathways contribution to VECP elicited by pseudorandom stimulation for a wider range of spatial frequencies. PMID:23940546

Multiple Sensory-Motor Pathways Lead to Coordinated Visual Attention

ERIC Educational Resources Information Center

Yu, Chen; Smith, Linda B.

2017-01-01

Joint attention has been extensively studied in the developmental literature because of overwhelming evidence that the ability to socially coordinate visual attention to an object is essential to healthy developmental outcomes, including language learning. The goal of this study was to understand the complex system of sensory-motor behaviors that…

Visual System Involvement in Patients with Friedreich's Ataxia

ERIC Educational Resources Information Center

Fortuna, Filippo; Barboni, Piero; Liguori, Rocco; Valentino, Maria Lucia; Savini, Giacomo; Gellera, Cinzia; Mariotti, Caterina; Rizzo, Giovanni; Tonon, Caterina; Manners, David; Lodi, Raffaele; Sadun, Alfredo A.; Carelli, Valerio

2009-01-01

Optic neuropathy is common in mitochondrial disorders, but poorly characterized in Friedreich's ataxia (FRDA), a recessive condition caused by lack of the mitochondrial protein frataxin. We investigated 26 molecularly confirmed FRDA patients by studying both anterior and posterior sections of the visual pathway using a new, integrated approach.…

Dynamic Visual Perception and Reading Development in Chinese School Children

ERIC Educational Resources Information Center

Meng, Xiangzhi; Cheng-Lai, Alice; Zeng, Biao; Stein, John F.; Zhou, Xiaolin

2011-01-01

The development of reading skills may depend to a certain extent on the development of basic visual perception. The magnocellular theory of developmental dyslexia assumes that deficits in the magnocellular pathway, indicated by less sensitivity in perceiving dynamic sensory stimuli, are responsible for a proportion of reading difficulties…

Helping Educators Find Visualizations and Teaching Materials Just-in-Time

NASA Astrophysics Data System (ADS)

McDaris, J.; Manduca, C. A.; MacDonald, R. H.

2005-12-01

Major events and natural disasters like hurricanes and tsunamis provide geoscience educators with powerful teachable moments to engage their students with class content. In order to take advantage of these opportunities, educators need quality topical resources related to current earth science events. The web has become an excellent vehicle for disseminating this type of resource. In response to the 2004 Indian Ocean Earthquake and to Hurricane Katrina's devastating impact on the US Gulf Coast, the On the Cutting Edge professional development program developed collections of visualizations for use in teaching. (serc.carleton.edu/NAGTWorkshops/visualization/collections/ tsunami.html,serc.carleton.edu/NAGTWorkshops/visualization/ collections/hurricanes.html). These sites are collections of links to visualizations and other materials that can support the efforts of faculty, teachers, and those engaged in public outreach. They bring together resources created by researchers, government agencies and respected media sources and organize them for easy use by educators. Links are selected to provide a variety of different types of visualizations (e.g photographic images, animations, satellite imagery) and to assist educators in teaching about the geologic event reported in the news, associated Earth science concepts, and related topics of high interest. The cited links are selected from quality sources and are reviewed by SERC staff before being included on the page. Geoscience educators are encouraged to recommend links and supporting materials and to comment on the available resources. In this way the collection becomes more complete and its quality is enhanced.. These sites have received substantial use (Tsunami - 77,000 visitors in the first 3 months, Hurricanes - 2500 visitors in the first week) indicating that in addition to use by educators, they are being used by the general public seeking information about the events. Thus they provide an effective mechanism for guiding the public to quality resources created by geoscience researchers and facilities, in addition to supporting incorporation of geoscience research in education.

A signaling visualization toolkit to support rational design of combination therapies and biomarker discovery: SiViT.

PubMed

Bown, James L; Shovman, Mark; Robertson, Paul; Boiko, Andrei; Goltsov, Alexey; Mullen, Peter; Harrison, David J

2017-05-02

Targeted cancer therapy aims to disrupt aberrant cellular signalling pathways. Biomarkers are surrogates of pathway state, but there is limited success in translating candidate biomarkers to clinical practice due to the intrinsic complexity of pathway networks. Systems biology approaches afford better understanding of complex, dynamical interactions in signalling pathways targeted by anticancer drugs. However, adoption of dynamical modelling by clinicians and biologists is impeded by model inaccessibility. Drawing on computer games technology, we present a novel visualization toolkit, SiViT, that converts systems biology models of cancer cell signalling into interactive simulations that can be used without specialist computational expertise. SiViT allows clinicians and biologists to directly introduce for example loss of function mutations and specific inhibitors. SiViT animates the effects of these introductions on pathway dynamics, suggesting further experiments and assessing candidate biomarker effectiveness. In a systems biology model of Her2 signalling we experimentally validated predictions using SiViT, revealing the dynamics of biomarkers of drug resistance and highlighting the role of pathway crosstalk. No model is ever complete: the iteration of real data and simulation facilitates continued evolution of more accurate, useful models. SiViT will make accessible libraries of models to support preclinical research, combinatorial strategy design and biomarker discovery.

Brain-wide pathway for waste clearance captured by contrast-enhanced MRI.

PubMed

Iliff, Jeffrey J; Lee, Hedok; Yu, Mei; Feng, Tian; Logan, Jean; Nedergaard, Maiken; Benveniste, Helene

2013-03-01

The glymphatic system is a recently defined brain-wide paravascular pathway for cerebrospinal fluid (CSF) and interstitial fluid (ISF) exchange that facilitates efficient clearance of solutes and waste from the brain. CSF enters the brain along para-arterial channels to exchange with ISF, which is in turn cleared from the brain along para-venous pathways. Because soluble amyloid β clearance depends on glymphatic pathway function, we proposed that failure of this clearance system contributes to amyloid plaque deposition and Alzheimer's disease progression. Here we provide proof of concept that glymphatic pathway function can be measured using a clinically relevant imaging technique. Dynamic contrast-enhanced MRI was used to visualize CSF-ISF exchange across the rat brain following intrathecal paramagnetic contrast agent administration. Key features of glymphatic pathway function were confirmed, including visualization of para-arterial CSF influx and molecular size-dependent CSF-ISF exchange. Whole-brain imaging allowed the identification of two key influx nodes at the pituitary and pineal gland recesses, while dynamic MRI permitted the definition of simple kinetic parameters to characterize glymphatic CSF-ISF exchange and solute clearance from the brain. We propose that this MRI approach may provide the basis for a wholly new strategy to evaluate Alzheimer's disease susceptibility and progression in the live human brain.

Brain-wide pathway for waste clearance captured by contrast-enhanced MRI

PubMed Central

Iliff, Jeffrey J.; Lee, Hedok; Yu, Mei; Feng, Tian; Logan, Jean; Nedergaard, Maiken; Benveniste, Helene

2013-01-01

The glymphatic system is a recently defined brain-wide paravascular pathway for cerebrospinal fluid (CSF) and interstitial fluid (ISF) exchange that facilitates efficient clearance of solutes and waste from the brain. CSF enters the brain along para-arterial channels to exchange with ISF, which is in turn cleared from the brain along para-venous pathways. Because soluble amyloid β clearance depends on glymphatic pathway function, we proposed that failure of this clearance system contributes to amyloid plaque deposition and Alzheimer’s disease progression. Here we provide proof of concept that glymphatic pathway function can be measured using a clinically relevant imaging technique. Dynamic contrast-enhanced MRI was used to visualize CSF-ISF exchange across the rat brain following intrathecal paramagnetic contrast agent administration. Key features of glymphatic pathway function were confirmed, including visualization of para-arterial CSF influx and molecular size-dependent CSF-ISF exchange. Whole-brain imaging allowed the identification of two key influx nodes at the pituitary and pineal gland recesses, while dynamic MRI permitted the definition of simple kinetic parameters to characterize glymphatic CSF-ISF exchange and solute clearance from the brain. We propose that this MRI approach may provide the basis for a wholly new strategy to evaluate Alzheimer’s disease susceptibility and progression in the live human brain. PMID:23434588

Dynamic reconfiguration of human brain functional networks through neurofeedback.

PubMed

Haller, Sven; Kopel, Rotem; Jhooti, Permi; Haas, Tanja; Scharnowski, Frank; Lovblad, Karl-Olof; Scheffler, Klaus; Van De Ville, Dimitri

2013-11-01

Recent fMRI studies demonstrated that functional connectivity is altered following cognitive tasks (e.g., learning) or due to various neurological disorders. We tested whether real-time fMRI-based neurofeedback can be a tool to voluntarily reconfigure brain network interactions. To disentangle learning-related from regulation-related effects, we first trained participants to voluntarily regulate activity in the auditory cortex (training phase) and subsequently asked participants to exert learned voluntary self-regulation in the absence of feedback (transfer phase without learning). Using independent component analysis (ICA), we found network reconfigurations (increases in functional network connectivity) during the neurofeedback training phase between the auditory target region and (1) the auditory pathway; (2) visual regions related to visual feedback processing; (3) insula related to introspection and self-regulation and (4) working memory and high-level visual attention areas related to cognitive effort. Interestingly, the auditory target region was identified as the hub of the reconfigured functional networks without a-priori assumptions. During the transfer phase, we again found specific functional connectivity reconfiguration between auditory and attention network confirming the specific effect of self-regulation on functional connectivity. Functional connectivity to working memory related networks was no longer altered consistent with the absent demand on working memory. We demonstrate that neurofeedback learning is mediated by widespread changes in functional connectivity. In contrast, applying learned self-regulation involves more limited and specific network changes in an auditory setup intended as a model for tinnitus. Hence, neurofeedback training might be used to promote recovery from neurological disorders that are linked to abnormal patterns of brain connectivity. Copyright © 2013 Elsevier Inc. All rights reserved.

Tectonigral Projections in the Primate: A Pathway for Pre-Attentive Sensory Input to Midbrain Dopaminergic Neurons

PubMed Central

May, Paul J.; McHaffie, John G.; Stanford, Terrence R.; Jiang, Huai; Costello, M. Gabriela; Coizet, Veronique; Hayes, Lauren M.; Haber, Suzanne N.; Redgrave, Peter

2010-01-01

Much of the evidence linking the short-latency phasic signaling of midbrain dopaminergic neurons with reward-prediction errors used in learning and habit formation comes from recording the visual responses of monkey dopaminergic neurons. However, the information encoded by dopaminergic neuron activity is constrained by the qualities of the afferent visual signals made available to these cells. Recent evidence from rats and cats indicates the primary source of this visual input originates subcortically, via a direct tectonigral projection. The present anatomical study sought to establish whether a direct tectonigral projection is a significant feature of the primate brain. Injections of anterograde tracers into the superior colliculus of macaque monkeys labelled terminal arbors throughout the substantia nigra, with the densest terminations in the dorsal tier. Labelled boutons were found in close association (possibly indicative of synaptic contact) with ventral midbrain neurons staining positively for the dopaminergic marker tyrosine hydroxylase. Injections of retrograde tracer confined to the macaque substantia nigra retrogradely labelled small to medium sized neurons in the intermediate and deep layers of the superior colliculus. Together, these data indicate that a direct tectonigral projection is also a feature of the monkey brain, and therefore likely to have been conserved throughout mammalian evolution. Insofar as the superior colliculus is configured to detect unpredicted, biologically salient, sensory events, it may be safer to regard the phasic responses of midbrain dopaminergic neurons as ‘sensory prediction errors’ rather than ‘reward prediction errors’, in which case, dopamine-based theories of reinforcement learning will require revision. PMID:19175405

Weighted link graphs: a distributed IDS for secondary intrusion detection and defense

NASA Astrophysics Data System (ADS)

Zhou, Mian; Lang, Sheau-Dong

2005-03-01

While a firewall installed at the perimeter of a local network provides the first line of defense against the hackers, many intrusion incidents are the results of successful penetration of the firewalls. One computer"s compromise often put the entire network at risk. In this paper, we propose an IDS that provides a finer control over the internal network. The system focuses on the variations of connection-based behavior of each single computer, and uses a weighted link graph to visualize the overall traffic abnormalities. The functionality of our system is of a distributed personal IDS system that also provides a centralized traffic analysis by graphical visualization. We use a novel weight assignment schema for the local detection within each end agent. The local abnormalities are quantitatively carried out by the node weight and link weight and further sent to the central analyzer to build the weighted link graph. Thus, we distribute the burden of traffic processing and visualization to each agent and make it more efficient for the overall intrusion detection. As the LANs are more vulnerable to inside attacks, our system is designed as a reinforcement to prevent corruption from the inside.

Effects of the AMPA Antagonist ZK 200775 on Visual Function: A Randomized Controlled Trial

PubMed Central

Bergholz, Richard; Staks, Thomas; Rüther, Klaus

2010-01-01

Background ZK 200775 is an antagonist at the α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionate (AMPA) receptor and had earned attention as a possible neuroprotective agent in cerebral ischemia. Probands receiving the agent within phase I trials reported on an alteration of visual perception. In this trial, the effects of ZK 200775 on the visual system were analyzed in detail. Methodology In a randomised controlled trial we examined eyes and vision before and after the intravenous administration of two different doses of ZK 200775 and placebo. There were 3 groups of 6 probands each: Group 1 recieved 0.03 mg/kg/h, group 2 0.75 mg/kg/h of ZK 200775, the control group received 0.9% sodium chloride solution. Probands were healthy males aged between 57 and 69 years. The following methods were applied: clinical examination, visual acuity, ophthalmoscopy, colour vision, rod absolute threshold, central visual field, pattern-reversal visual evoked potentials (pVEP), ON-OFF and full-field electroretinogram (ERG). Principal Findings No effect of ZK 200775 was seen on eye position or motility, stereopsis, pupillary function or central visual field testing. Visual acuity and dark vision deteriorated significantly in both treated groups. Color vision was most remarkably impaired. The dark-adapted ERG revealed a reduction of oscillatory potentials (OP) and partly of the a- and b-wave, furthermore an alteration of b-wave morphology and an insignificantly elevated b/a-ratio. Cone-ERG modalities showed decreased amplitudes and delayed implicit times. In the ON-OFF ERG the ON-answer amplitudes increased whereas the peak times of the OFF-answer were reduced. The pattern VEP exhibited lower amplitudes and prolonged peak times. Conclusions The AMPA receptor blockade led to a strong impairment of typical OFF-pathway functions like color vision and the cone ERG. On the other hand the ON-pathway as measured by dark vision and the scotopic ERG was affected as well. This further elucidates the interdependence of both pathways. Trial Registration ClinicalTrials.gov NCT00999284 PMID:20711429

Developmental Dyslexia: Exploring How Much Phonological and Visual Attention Span Disorders Are Linked to Simultaneous Auditory Processing Deficits

ERIC Educational Resources Information Center

Lallier, Marie; Donnadieu, Sophie; Valdois, Sylviane

2013-01-01

The simultaneous auditory processing skills of 17 dyslexic children and 17 skilled readers were measured using a dichotic listening task. Results showed that the dyslexic children exhibited difficulties reporting syllabic material when presented simultaneously. As a measure of simultaneous visual processing, visual attention span skills were…

Visual Analytics in Public Safety: Example Capabilities for Example Government Agencies

DTIC Science & Technology

2011-10-01

is not limited to: the Police Records Information Management Environment for British Columbia (PRIME-BC), the Police Reporting and Occurrence System...and filtering for rapid identification of relevant documents - Graphical environment for visual evidence marshaling - Interactive linking and...analytical reasoning facilitated by interactive visual interfaces and integration with computational analytics. Indeed, a wide variety of technologies

Visual Form, Ethics, and a Typology of Purpose: Teaching Effective Information Design

ERIC Educational Resources Information Center

Rosenquist, Christina

2012-01-01

Stallworth Williams introduces concepts of visual rhetoric and ethics for a classroom exercise in the analysis and revision of a sales letter. This article revisits Stallworth Williams's proposed teaching strategies, suggesting that not only do students need to be instructed in elements of visual design, but they must also be taught to link those…

VIPER: Virtual Intelligent Planetary Exploration Rover

NASA Technical Reports Server (NTRS)

Edwards, Laurence; Flueckiger, Lorenzo; Nguyen, Laurent; Washington, Richard

2001-01-01

Simulation and visualization of rover behavior are critical capabilities for scientists and rover operators to construct, test, and validate plans for commanding a remote rover. The VIPER system links these capabilities. using a high-fidelity virtual-reality (VR) environment. a kinematically accurate simulator, and a flexible plan executive to allow users to simulate and visualize possible execution outcomes of a plan under development. This work is part of a larger vision of a science-centered rover control environment, where a scientist may inspect and explore the environment via VR tools, specify science goals, and visualize the expected and actual behavior of the remote rover. The VIPER system is constructed from three generic systems, linked together via a minimal amount of customization into the integrated system. The complete system points out the power of combining plan execution, simulation, and visualization for envisioning rover behavior; it also demonstrates the utility of developing generic technologies. which can be combined in novel and useful ways.

Visualizing pathogen internalization pathways in fresh tomatoes using MicroCT and confocal laser scanning microscopy

USDA-ARS?s Scientific Manuscript database

Pathogen contamination of fresh produce significantly impacts public health and the produce industry's economic well-being. In tomato fruits, studies have shown that the stem-scar plays an important role in pathogen infiltration. However, the exact mechanisms and pathways for pathogen movement insi...

Assessment of visual disability using visual evoked potentials.

PubMed

Jeon, Jihoon; Oh, Seiyul; Kyung, Sungeun

2012-08-06

The purpose of this study is to validate the use of visual evoked potential (VEP) to objectively quantify visual acuity in normal and amblyopic patients, and determine if it is possible to predict visual acuity in disability assessment to register visual pathway lesions. A retrospective chart review was conducted of patients diagnosed with normal vision, unilateral amblyopia, optic neuritis, and visual disability who visited the university medical center for registration from March 2007 to October 2009. The study included 20 normal subjects (20 right eyes: 10 females, 10 males, ages 9-42 years), 18 unilateral amblyopic patients (18 amblyopic eyes, ages 19-36 years), 19 optic neuritis patients (19 eyes: ages 9-71 years), and 10 patients with visual disability having visual pathway lesions. Amplitude and latencies were analyzed and correlations with visual acuity (logMAR) were derived from 20 normal and 18 amblyopic subjects. Correlation of VEP amplitude and visual acuity (logMAR) of 19 optic neuritis patients confirmed relationships between visual acuity and amplitude. We calculated the objective visual acuity (logMAR) of 16 eyes from 10 patients to diagnose the presence or absence of visual disability using relations derived from 20 normal and 18 amblyopic eyes. Linear regression analyses between amplitude of pattern visual evoked potentials and visual acuity (logMAR) of 38 eyes from normal (right eyes) and amblyopic (amblyopic eyes) subjects were significant [y = -0.072x + 1.22, x: VEP amplitude, y: visual acuity (logMAR)]. There were no significant differences between visual acuity prediction values, which substituted amplitude values of 19 eyes with optic neuritis into function. We calculated the objective visual acuity of 16 eyes of 10 patients to diagnose the presence or absence of visual disability using relations of y = -0.072x + 1.22 (-0.072). This resulted in a prediction reference of visual acuity associated with malingering vs. real disability in a range >5.77 μV. The results could be useful, especially in cases of no obvious pale disc with trauma. Visual acuity quantification using absolute value of amplitude in pattern visual evoked potentials was useful in confirming subjective visual acuity for cutoff values >5.77 μV in disability evaluation to discriminate the malingering from real disability.

Assessment of visual disability using visual evoked potentials

PubMed Central

2012-01-01

Background The purpose of this study is to validate the use of visual evoked potential (VEP) to objectively quantify visual acuity in normal and amblyopic patients, and determine if it is possible to predict visual acuity in disability assessment to register visual pathway lesions. Methods A retrospective chart review was conducted of patients diagnosed with normal vision, unilateral amblyopia, optic neuritis, and visual disability who visited the university medical center for registration from March 2007 to October 2009. The study included 20 normal subjects (20 right eyes: 10 females, 10 males, ages 9–42 years), 18 unilateral amblyopic patients (18 amblyopic eyes, ages 19–36 years), 19 optic neuritis patients (19 eyes: ages 9–71 years), and 10 patients with visual disability having visual pathway lesions. Amplitude and latencies were analyzed and correlations with visual acuity (logMAR) were derived from 20 normal and 18 amblyopic subjects. Correlation of VEP amplitude and visual acuity (logMAR) of 19 optic neuritis patients confirmed relationships between visual acuity and amplitude. We calculated the objective visual acuity (logMAR) of 16 eyes from 10 patients to diagnose the presence or absence of visual disability using relations derived from 20 normal and 18 amblyopic eyes. Results Linear regression analyses between amplitude of pattern visual evoked potentials and visual acuity (logMAR) of 38 eyes from normal (right eyes) and amblyopic (amblyopic eyes) subjects were significant [y = −0.072x + 1.22, x: VEP amplitude, y: visual acuity (logMAR)]. There were no significant differences between visual acuity prediction values, which substituted amplitude values of 19 eyes with optic neuritis into function. We calculated the objective visual acuity of 16 eyes of 10 patients to diagnose the presence or absence of visual disability using relations of y = −0.072x + 1.22 (−0.072). This resulted in a prediction reference of visual acuity associated with malingering vs. real disability in a range >5.77 μV. The results could be useful, especially in cases of no obvious pale disc with trauma. Conclusions Visual acuity quantification using absolute value of amplitude in pattern visual evoked potentials was useful in confirming subjective visual acuity for cutoff values >5.77 μV in disability evaluation to discriminate the malingering from real disability. PMID:22866948

Analysis of Differentially Expressed Genes and Signaling Pathways Related to Intramuscular Fat Deposition in Skeletal Muscle of Sex-Linked Dwarf Chickens

PubMed Central

Ye, Yaqiong; Lin, Shumao; Mu, Heping; Tang, Xiaohong; Ou, Yangdan; Chen, Jian; Ma, Yongjiang; Li, Yugu

2014-01-01

Intramuscular fat (IMF) plays an important role in meat quality. However, the molecular mechanisms underlying IMF deposition in skeletal muscle have not been addressed for the sex-linked dwarf (SLD) chicken. In this study, potential candidate genes and signaling pathways related to IMF deposition in chicken leg muscle tissue were characterized using gene expression profiling of both 7-week-old SLD and normal chickens. A total of 173 differentially expressed genes (DEGs) were identified between the two breeds. Subsequently, 6 DEGs related to lipid metabolism or muscle development were verified in each breed based on gene ontology (GO) analysis. In addition, KEGG pathway analysis of DEGs indicated that some of them (GHR, SOCS3, and IGF2BP3) participate in adipocytokine and insulin signaling pathways. To investigate the role of the above signaling pathways in IMF deposition, the gene expression of pathway factors and other downstream genes were measured by using qRT-PCR and Western blot analyses. Collectively, the results identified potential candidate genes related to IMF deposition and suggested that IMF deposition in skeletal muscle of SLD chicken is regulated partially by pathways of adipocytokine and insulin and other downstream signaling pathways (TGF-β/SMAD3 and Wnt/catenin-β pathway). PMID:24757673

Blindsight and Unconscious Vision: What They Teach Us about the Human Visual System

PubMed Central

Ajina, Sara; Bridge, Holly

2017-01-01

Damage to the primary visual cortex removes the major input from the eyes to the brain, causing significant visual loss as patients are unable to perceive the side of the world contralateral to the damage. Some patients, however, retain the ability to detect visual information within this blind region; this is known as blindsight. By studying the visual pathways that underlie this residual vision in patients, we can uncover additional aspects of the human visual system that likely contribute to normal visual function but cannot be revealed under physiological conditions. In this review, we discuss the residual abilities and neural activity that have been described in blindsight and the implications of these findings for understanding the intact system. PMID:27777337

[Multifocal visual electrophysiology in visual function evaluation].

PubMed

Peng, Shu-Ya; Chen, Jie-Min; Liu, Rui-Jue; Zhou, Shu; Liu, Dong-Mei; Xia, Wen-Tao

2013-08-01

Multifocal visual electrophysiology, consisting of multifocal electroretinography (mfERG) and multifocal visual evoked potential (mfVEP), can objectively evaluate retina function and retina-cortical conduction pathway status by stimulating many local retinal regions and obtaining each local response simultaneously. Having many advantages such as short testing time and high sensitivity, it has been widely used in clinical ophthalmology, especially in the diagnosis of retinal disease and glaucoma. It is a new objective technique in clinical forensic medicine involving visual function evaluation of ocular trauma in particular. This article summarizes the way of stimulation, the position of electrodes, the way of analysis, the visual function evaluation of mfERG and mfVEP, and discussed the value of multifocal visual electrophysiology in forensic medicine.

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

PubMed Central

Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

2011-01-01

Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. Results: The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and ‘wet lab’ scientists. Availability and implementation: The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X. Contact: duccio.cavalieri@unifi.it; sorin@wayne.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21653523

Imaging axonal transport in the rat visual pathway.

PubMed

Abbott, Carla J; Choe, Tiffany E; Lusardi, Theresa A; Burgoyne, Claude F; Wang, Lin; Fortune, Brad

2013-02-01

A technique was developed for assaying axonal transport in retinal ganglion cells using 2 µl injections of 1% cholera toxin b-subunit conjugated to AlexaFluor488 (CTB). In vivo retinal and post-mortem brain imaging by confocal scanning laser ophthalmoscopy and post-mortem microscopy were performed. The transport of CTB was sensitive to colchicine, which disrupts axonal microtubules. The bulk rates of transport were determined to be approximately 80-90 mm/day (anterograde) and 160 mm/day (retrograde). Results demonstrate that axonal transport of CTB can be monitored in vivo in the rodent anterior visual pathway, is dependent on intact microtubules, and occurs by active transport mechanisms.

Flavopiridol in Treating Children With Relapsed or Refractory Solid Tumors or Lymphomas

ClinicalTrials.gov

2013-07-01

Recurrent Childhood Brain Stem Glioma; Recurrent Childhood Cerebellar Astrocytoma; Recurrent Childhood Cerebral Astrocytoma; Recurrent Childhood Ependymoma; Recurrent Childhood Large Cell Lymphoma; Recurrent Childhood Liver Cancer; Recurrent Childhood Lymphoblastic Lymphoma; Recurrent Childhood Malignant Germ Cell Tumor; Recurrent Childhood Medulloblastoma; Recurrent Childhood Rhabdomyosarcoma; Recurrent Childhood Small Noncleaved Cell Lymphoma; Recurrent Childhood Soft Tissue Sarcoma; Recurrent Childhood Supratentorial Primitive Neuroectodermal Tumor; Recurrent Childhood Visual Pathway and Hypothalamic Glioma; Recurrent Childhood Visual Pathway Glioma; Recurrent Ewing Sarcoma/Peripheral Primitive Neuroectodermal Tumor; Recurrent Neuroblastoma; Recurrent Osteosarcoma; Recurrent Retinoblastoma; Recurrent Wilms Tumor and Other Childhood Kidney Tumors; Recurrent/Refractory Childhood Hodgkin Lymphoma; Unspecified Childhood Solid Tumor, Protocol Specific

SIGNALING PATHWAYS IN MELANOSOME BIOGENESIS AND PATHOLOGY

PubMed Central

Schiaffino, Maria Vittoria

2010-01-01

Melanosomes are the specialized intracellular organelles of pigment cells devoted to the synthesis, storage and transport of melanin pigments, which are responsible for most visible pigmentation in mammals and other vertebrates. As a direct consequence, any genetic mutation resulting in alteration of melanosomal function, either because affecting pigment cell survival, migration and differentiation, or because interfering with melanosome biogenesis, transport and transfer to keratinocytes, is immediately translated into color variations of skin, fur, hair or eyes. Thus, over one hundred genes and proteins have been identified as pigmentary determinants in mammals, providing us with a deep understanding of this biological system, which functions by using mechanisms and processes that have parallels in other tissues and organs. In particular, many genes implicated in melanosome biogenesis have been characterized, so that melanosomes represent an incredible source of information and a model for organelles belonging to the secretory pathway. Furthermore, the function of melanosomes can be associated with common physiological phenotypes, such as variation of pigmentation among individuals, and with rare pathological conditions, such as albinism, characterized by severe visual defects. Among the most relevant mechanisms operating in melanosome biogenesis are the signal transduction pathways mediated by two peculiar G protein-coupled receptors: the melanocortin-1 receptor (MC1R), involved in the fair skin/red hair phenotype and skin cancer; and OA1 (GPR143), whose loss-of-function results in X-linked ocular albinism. This review will focus on the most recent novelties regarding the functioning of these two receptors, by highlighting emerging signaling mechanisms and general implications for cell biology and pathology. PMID:20381640

Detection of differentially expressed genes in broiler pectoralis major muscle affected by White Striping - Wooden Breast myopathies.

PubMed

Zambonelli, Paolo; Zappaterra, Martina; Soglia, Francesca; Petracci, Massimiliano; Sirri, Federico; Cavani, Claudio; Davoli, Roberta

2016-12-01

White Striping and Wooden Breast (WS/WB) are abnormalities increasingly occurring in the fillets of high breast yield and growth rate chicken hybrids. These defects lead to consistent economic losses for poultry meat industry, as affected broiler fillets present an impaired visual appearance that negatively affects consumers' acceptability. Previous studies have highlighted in affected fillets a severely damaged muscle, showing profound inflammation, fibrosis, and lipidosis. The present study investigated the differentially expressed genes and pathways linked to the compositional changes observed in WS/WB breast muscles, in order to outline a more complete framework of the gene networks related to the occurrence of this complex pathological picture. The biochemical composition was performed on 20 pectoralis major samples obtained from high breast yield and growth rate broilers (10 affected vs. 10 normal) and 12 out of the 20 samples were used for the microarray gene expression profiling (6 affected vs. 6 normal). The obtained results indicate strong changes in muscle mineral composition, coupled to an increased deposition of fat. In addition, 204 differentially expressed genes (DEG) were found: 102 up-regulated and 102 down-regulated in affected breasts. The gene expression pathways found more altered in WS/WB muscles are those related to muscle development, polysaccharide metabolic processes, proteoglycans synthesis, inflammation, and calcium signaling pathway. On the whole, the findings suggest that a multifactorial and complex etiology is associated with the occurrence of WS/WB muscle abnormalities, contributing to further defining the transcription patterns associated with these myopathies. © 2016 Poultry Science Association Inc.

Genetic influences on the neural basis of social cognition

PubMed Central

Skuse, David

2006-01-01

The neural basis of social cognition has been the subject of intensive research in both human and non-human primates. Exciting, provocative and yet consistent findings are emerging. A major focus of interest is the role of efferent and afferent connectivity between the amygdala and the neocortical brain regions, now believed to be critical for the processing of social and emotional perceptions. One possible component is a subcortical neural pathway, which permits rapid and preconscious processing of potentially threatening stimuli, and it leads from the retina to the superior colliculus, to the pulvinar nucleus of the thalamus and then to the amygdala. This pathway is activated by direct eye contact, one of many classes of potential threat, and may be particularly responsive to the ‘whites of the eyes’. In humans, autonomic arousal evoked by this stimulus is associated with the activity in specific cortical regions concerned with processing visual information from faces. The integrated functioning of these pathways is modulated by one or more X-linked genes, yet to be identified. The emotional responsiveness of the amygdala, and its associated circuits, to social threat is also influenced by functional polymorphisms in the promoter of the serotonin transporter gene. We still do not have a clear account of how specific allelic variation, in candidate genes, increases susceptibility to developmental disorders, such as autism, or psychiatric conditions, such as anxiety or depressive illness. However, the regulation of emotional responsiveness to social cues lies at the heart of the problem, and recent research indicates that we may be nearing a deeper and more comprehensive understanding. PMID:17118928

Unusual phenotypic expression of an XLRS1 mutation in X-linked juvenile retinoschisis.

PubMed

Dodds, Jodi A; Srivastava, Anand K; Holden, Kenton R

2006-04-01

X-linked juvenile retinoschisis is a rare progressive vitreoretinal degenerative process that appears in early childhood, results in decreased visual acuity and blindness (if severe), and is caused by various mutations within the XLRS1 gene at Xp22.2. We report an affected family of Western European ancestry with X-linked juvenile retinoschisis. The family was found to carry a 304C-->T substitution in exon 4 of the XLRS1 gene, resulting in an Arg102Trp amino acid substitution. Two of the four available clinical cases in this family were found to carry the mutation. All available mothers of affected males were found to be unaffected carriers of the mutation, a typical feature of X-linked diseases. Two new female carriers, sisters of affected males, were identified and counseled accordingly. Questionnaires on visual functioning were given to the affected family members to examine the psychologic and sociologic impact of X-linked juvenile retinoschisis, which documented an associated stigma even when affected with a "mild" phenotype.

Functionally defined white matter reveals segregated pathways in human ventral temporal cortex associated with category-specific processing

PubMed Central

Gomez, Jesse; Pestilli, Franco; Witthoft, Nathan; Golarai, Golijeh; Liberman, Alina; Poltoratski, Sonia; Yoon, Jennifer; Grill-Spector, Kalanit

2014-01-01

Summary It is unknown if the white matter properties associated with specific visual networks selectively affect category-specific processing. In a novel protocol we combined measurements of white matter structure, functional selectivity, and behavior in the same subjects. We find two parallel white matter pathways along the ventral temporal lobe connecting to either face-selective or place-selective regions. Diffusion properties of portions of these tracts adjacent to face- and place-selective regions of ventral temporal cortex correlate with behavioral performance for face or place processing, respectively. Strikingly, adults with developmental prosopagnosia (face blindness) express an atypical structure-behavior relationship near face-selective cortex, suggesting that white matter atypicalities in this region may have behavioral consequences. These data suggest that examining the interplay between cortical function, anatomical connectivity, and visual behavior is integral to understanding functional networks and their role in producing visual abilities and deficits. PMID:25569351

Primary Central Nervous System Lymphoma of Optic Chiasma: Endoscopic Endonasal Treatment.

PubMed

Ozdemir, Evin Singar; Yildirim, Ali Erdem; Can, Aslihan Yavas

2018-01-01

Isolated primary central nervous system lymphoma arising from anterior visual pathway is very rare. A 76-year-old immunocompetent previously healthy man presented bilateral decreased visual acuity in 1 month. Pituitary magnetic resonans imaging (MRI) showed a lobulated mass with homogeneous enhancement after gadolinium administration that arising from optic chiasm suggested that inflammatory disease or an optic glioma. The patient underwent an extended endoscopic endonasal transsphenoidal surgery. Postoperative course and outcomes were wonderful. Histopathological diagnosis was diffuse large B-cell lymphoma. The patient underwent investigations for systemic lymphomatous involvement, did not detect any evidence of systemic disease. In this case, we claimed that differential diagnoses of anterior visual pathway lesions are difficult because of similarity of lesions on clinical and radiological examinations. Biopsy is essential for these lesions. As a biopsy technique, endoscopic endonasal transsphenoidal approach is safer and more effective than open procedures.

A computational exploration of complementary learning mechanisms in the primate ventral visual pathway.

PubMed

Spoerer, Courtney J; Eguchi, Akihiro; Stringer, Simon M

2016-02-01

In order to develop transformation invariant representations of objects, the visual system must make use of constraints placed upon object transformation by the environment. For example, objects transform continuously from one point to another in both space and time. These two constraints have been exploited separately in order to develop translation and view invariance in a hierarchical multilayer model of the primate ventral visual pathway in the form of continuous transformation learning and temporal trace learning. We show for the first time that these two learning rules can work cooperatively in the model. Using these two learning rules together can support the development of invariance in cells and help maintain object selectivity when stimuli are presented over a large number of locations or when trained separately over a large number of viewing angles. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Tracking the allocation of attention using human pupillary oscillations

PubMed Central

Naber, Marnix; Alvarez, George A.; Nakayama, Ken

2013-01-01

The muscles that control the pupil are richly innervated by the autonomic nervous system. While there are central pathways that drive pupil dilations in relation to arousal, there is no anatomical evidence that cortical centers involved with visual selective attention innervate the pupil. In this study, we show that such connections must exist. Specifically, we demonstrate a novel Pupil Frequency Tagging (PFT) method, where oscillatory changes in stimulus brightness over time are mirrored by pupil constrictions and dilations. We find that the luminance–induced pupil oscillations are enhanced when covert attention is directed to the flicker stimulus and when targets are correctly detected in an attentional tracking task. These results suggest that the amplitudes of pupil responses closely follow the allocation of focal visual attention and the encoding of stimuli. PFT provides a new opportunity to study top–down visual attention itself as well as identifying the pathways and mechanisms that support this unexpected phenomenon. PMID:24368904