Matching visual induction effects on screens of different size.
Ontology highlight
ABSTRACT:
SUBMITTER: Canham T
PROVIDER: S-EPMC8237091 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:BACKGROUND: RNA interference (RNAi) has been seen as a revolution in functional genomics and system biology. Genome-wide RNAi research relies on the development of RNAi high-throughput screening (HTS) assays. One of the most fundamental challenges in RNAi HTS is to glean biological significance from mounds of data, which relies on the development of effective analytic methods for selecting effective small interfering RNAs (siRNAs). FINDINGS: Based on a recently proposed parameter, strictly standardized mean difference (SSMD), I propose an analytic method for genome-wide screens of effective siRNAs through assessing and testing the size of siRNA effects. Central to this method is the capability of SSMD in quantifying siRNA effects. This method has relied on normal approximation, which works only in the primary screens but not in the confirmatory screens. In this paper, I explore the non-central t-distribution property of SSMD estimates and use this property to extend the SSMD-based method so that it works effectively in either primary or confirmatory screens as well as in any HTS screens with or without replicates. The SSMD-based method maintains a balanced control of false positives and false negatives. CONCLUSION: The central interest in genome-wide RNAi research is the selection of effective siRNAs which relies on the development of analytic methods to measure the size of siRNA effects. The new analytic method for hit selection provided in this paper offers a good analytic tool for selecting effective siRNAs, better than current analytic methods, and thus may have broad utility in genome-wide RNAi research.
| S-EPMC2526086 | biostudies-other
Project description:Defaunation by humans causes a loss of large animals in many ecosystems globally. Recent work has emphasized the consequences of downsizing in animal communities for ecosystem functioning. However, no study so far has integrated network theory and life-history trade-offs to mechanistically evaluate the functional consequences of defaunation in plant-animal networks. Here, we simulated an avian seed-dispersal network and its derived ecosystem function seedling recruitment to assess the relative importance of different size-related mechanisms. Specifically, we considered size matching (between bird size and seed size) and size trade-offs, which are driven by differences in plant or animal species abundance (negative size-quantity relationship) as well as in recruitment probability and disperser quality (positive size-quality relationship). Defaunation led to impoverished seedling communities in terms of diversity and seed size, but only if models accounted for size matching. In addition, size trade-off in plants, in concert with size matching, provoked rapid decays in seedling abundance in response to defaunation. These results underscore a disproportional importance of large animals for ecosystem functions. Downsizing in ecological networks will have severe consequences for ecosystem functioning, especially in interaction networks that are structured by size matching between plants and animals.
| S-EPMC5454253 | biostudies-literature
Project description:Auditory-guided vocal learning is a mechanism that operates both in humans and other animal species making us capable to imitate arbitrary sounds. Both auditory memories and auditory feedback interact to guide vocal learning. This may explain why it is easier for humans to imitate the pitch of a human voice than the pitch of a synthesized sound. In this study, we compared the effects of two different feedback modalities in learning pitch-matching abilities using a synthesized pure tone in 47 participants with no prior music experience. Participants were divided into three groups: a feedback group (N = 15) receiving real-time visual feedback of their pitch as well as knowledge of results; an equal-timbre group (N = 17) receiving additional auditory feedback of the target note with a similar timbre to the instrument being used (i.e., violin or human voice); and a control group (N = 15) practicing without any feedback or knowledge of results. An additional fourth group of violin experts performed the same task for comparative purposes (N = 15). All groups were posteriorly evaluated in a transfer phase. Both experimental groups (i.e., the feedback and equal-timbre groups) improved their intonation abilities with the synthesized sound after receiving feedback. Participants from the equal-timber group seemed as capable as the feedback group of producing the required pitch with the voice after listening to the human voice, but not with the violin (although they also showed improvement). In addition, only participants receiving real-time visual feedback learned and retained in the transfer phase the mapping between the synthesized pitch and its correspondence with the produced vocal or violin pitch. It is suggested that both the effect of an objective external reward, together with the experience of exploring the pitch space with their instrument in an explicit manner, helped participants to understand how to control their pitch production, strengthening their schemas, and favoring retention.
| S-EPMC8297736 | biostudies-literature
Project description:The purpose of this study was to investigate the influence of smartphone reading on the ocular surface and to compare the various effects of different screens and light conditions on the ocular surface. One hundred nineteen volunteers were randomly divided into: light + organic light-emitting diode (OLED), light + electronic ink (eINK), dark + OLED, and dark + eINK. Ocular surface examinations, including noninvasive break-up time (NIBUT), noninvasive keratograph tear meniscus height (NIKTMH), ocular redness, fluorescein break-up time (FBUT), corneal fluorescein staining, meibomian gland assessment, Schirmer I Test, and blinking frequency, were performed before and after a reading task. Symptoms were evaluated using the Ocular Surface Disease Index (OSDI) and Computer Vision Syndrome Questionnaire (CVS-Q). NIBUT and FBUT were decreased statistically significantly after participants read on an OLED screen for 2 hours compared with the baseline in light and dark environments, whereas no statistically significant decrease was observed on an eINK screen. NIKTMH was statistically significantly decreased after reading on an OLED screen in light and dark settings, and the eINK screen had a lesser effect on NIKTMH. An obvious increase in the ocular redness, OSDI and CVS-Q scores was observed after reading on an OLED screen, whereas the eINK screen had a lesser effect on these indicators. Blink rate increased gradually in OLED subgroups during the reading task, whereas no statistically significant difference was observed in the eINK subgroups. Our research suggested that reading on an OLED screen can cause ocular surface disorder and obvious subjective discomfort, whereas reading on an eINK screen can minimize ocular surface disorder in both dark and light environments.
| S-EPMC8212737 | biostudies-literature
Project description:Encoding precision in visual working memory decreases with the number of encoded items. Here, we propose a normative theory for such set size effects: the brain minimizes a weighted sum of an error-based behavioral cost and a neural encoding cost. We construct a model from this theory and find that it predicts set size effects. Notably, these effects are mediated by probing probability, which aligns with previous empirical findings. The model accounts well for effects of both set size and probing probability on encoding precision in nine delayed-estimation experiments. Moreover, we find support for the prediction that the total amount of invested resource can vary non-monotonically with set size. Finally, we show that it is sometimes optimal to encode only a subset or even none of the relevant items in a task. Our findings raise the possibility that cognitive "limitations" arise from rational cost minimization rather than from constraints.
| S-EPMC6110611 | biostudies-literature
Project description:Factors influencing crossmodal interactions are manifold and operate in a stimulus-driven, bottom-up fashion, as well as via top-down control. Here, we evaluate the interplay of stimulus congruence and attention in a visual-tactile task. To this end, we used a matching paradigm requiring the identification of spatial patterns that were concurrently presented visually on a computer screen and haptically to the fingertips by means of a Braille stimulator. Stimulation in our paradigm was always bimodal with only the allocation of attention being manipulated between conditions. In separate blocks of the experiment, participants were instructed to (a) focus on a single modality to detect a specific target pattern, (b) pay attention to both modalities to detect a specific target pattern, or (c) to explicitly evaluate if the patterns in both modalities were congruent or not. For visual as well as tactile targets, congruent stimulus pairs led to quicker and more accurate detection compared to incongruent stimulation. This congruence facilitation effect was more prominent under divided attention. Incongruent stimulation led to behavioral decrements under divided attention as compared to selectively attending a single sensory channel. Additionally, when participants were asked to evaluate congruence explicitly, congruent stimulation was associated with better performance than incongruent stimulation. Our results extend previous findings from audiovisual studies, showing that stimulus congruence also resulted in behavioral improvements in visuotactile pattern matching. The interplay of stimulus processing and attentional control seems to be organized in a highly flexible fashion, with the integration of signals depending on both bottom-up and top-down factors, rather than occurring in an 'all-or-nothing' manner.
| S-EPMC4159283 | biostudies-literature
Project description:When an observer scans the visual surround, the images cast on the two retinae are slightly different due to the different viewpoints of the two eyes. Objects in the horizontal plane of regard can be seen single by aligning the lines of sight without changing the torsional stance of the eyes. Due to the peculiar ocular kinematics this is not possible for objects above or below the horizontal plane of regard. We provide evidence that binocular fusion can be achieved independently of viewing direction by adjusting the mutual torsional orientation of the eyes in the frontal plane. We characterize the fusion positions of the eyes across the oculomotor range by deriving simple trigonometric equations for the required torsion as a function of gaze direction and compute the iso-torsion contours yielding binocular fusion. Finally, we provide experimental evidence that eye positions in far-to-near re-fixation saccades indeed converge towards the predicted positions by adjusting the torsion of the eyes. This is the first report that describes the three-dimensional orientation of the eyes at binocular fusion positions based on the three-dimensional ocular kinematics. It closes a gap between the sensory and the motor side of binocular vision and stereoscopy.
| S-EPMC6045635 | biostudies-literature
Project description:A mild traumatic brain injury is a neurological disturbance of transient or/and chronic nature after a direct blow of the head/neck or exposure of the body to impulsive biomechanical forces, indirectly affecting the brain. The neuropathological events leading to the clinical signs, symptoms and functional disturbances are still elusive due to a lack of sensitive brain-screening tools. Animal models offer the potential to study neural pathomechanisms in close detail. We recently proposed a non-invasive protocol for inducing concussion-like symptoms in larval zebrafish via exposure to rapid linearly accelerating-decelerating body motion. By mean of auditory 'startle reflex habituation' assessments-an established neurophysiological health index-we probed acute and chronic effects that mirror human concussion patterns. This study aimed at expanding our previous work by assessing the ensuing effects with visual-as opposed to auditory-'startle reflex habituation' quantifications, by using the same methodology. We observed that immediately after impact exposure, the fish showed impaired sensory reactivity and smaller decay constant, possibly mirroring acute signs of confusion or loss of consciousness in humans. By 30-min post-injury, the fish display temporary signs of visual hypersensitivity, manifested as increased visuomotor reactivity and a relatively enlarged decay constant, putatively reflecting human post-concussive sign of visual hypersensitivity. In the following 5-24 h, the exposed fish progressively develop chronic signs of CNS dysfunction, in the form of low startle responsivity. However, the preserved decay constant suggests that neuroplastic changes may occur to restore CNS functioning after undergoing the 'concussive procedure'. The observed findings expand our previous work providing further behavioural evidence for the model. Limitations that still require addressment are discussed, advancing further behavioural and microscopic analyses that would be necessary for the validation of the model in its putative relatability with human concussion.
| S-EPMC10065185 | biostudies-literature
Project description:Abstract:The visual system is highly variable across species, and such variability is a key factor influencing animal behavior. Variation in the visual system, for instance, can influence the outcome of learning tasks when visual stimuli are used. We illustrate this issue in guppies (Poecilia reticulata) artificially selected for large and small relative brain size with pronounced behavioral differences in learning experiments and mate choice tests. We performed a study of the visual system by quantifying eye size and optomotor response of large-brained and small-brained guppies. This represents the first experimental test of the link between brain size evolution and visual acuity. We found that female guppies have larger eyes than male guppies, both in absolute terms and in relation to their body size. Likewise, individuals selected for larger brains had slightly larger eyes but not better visual acuity than small-brained guppies. However, body size was positively associated with visual acuity. We discuss our findings in relation to previous macroevolutionary studies on the evolution of brain morphology, eye morphology, visual acuity, and ecological variables, while stressing the importance of accounting for sensory abilities in behavioral studies. Significance statement:Pre-existing perceptual biases can be keys for the development of specific behavioral patterns. Hence, potential differences in sensory systems need to be taken into account in the study of animal behavior. We highlight this necessity concentrating on the visual domain and using experimental data on brain size-selected guppies in which we assessed eye size and visual acuity. Behavioral differences between large-brained and small-brained guppies in learning and mate choice predominantly relied on tests using visual cues. Analyses of visual capabilities in this system are therefore necessary. Furthermore, this system offers the unprecedented opportunity to experimentally test the relationship between brain size, eye morphology, and visual capabilities. Our results show similar visual acuities between large-brained and small-brained guppies. However, the differences observed in eye area between the sexes, together with the observed positive relationship between body size and visual acuity, highlight the need to incorporate perceptive differences in the study of animal behavior.
| S-EPMC5705735 | biostudies-literature
Project description:BackgroundOntology matching seeks to find semantic correspondences between ontologies. With an increasing number of biomedical ontologies being developed independently, matching these ontologies to solve the interoperability problem has become a critical task in biomedical applications. However, some challenges remain. First, extracting and constructing matching clues from biomedical ontologies is a nontrivial problem. Second, it is unknown whether there are dominant matchers while matching biomedical ontologies. Finally, ontology matching also suffers from computational complexity owing to the large-scale sizes of biomedical ontologies.ObjectiveTo investigate the effectiveness of matching clues and composite match approaches, this paper presents a spectrum of matchers with different combination strategies and empirically studies their influence on matching biomedical ontologies. Besides, extended reduction anchors are introduced to effectively decrease the time complexity while matching large biomedical ontologies.MethodsIn this paper, atomic and composite matching clues are first constructed in 4 dimensions: terminology, structure, external knowledge, and representation learning. Then, a spectrum of matchers based on a flexible combination of atomic clues are designed and utilized to comprehensively study the effectiveness. Besides, we carry out a systematic comparative evaluation of different combinations of matchers. Finally, extended reduction anchor is proposed to significantly alleviate the time complexity for matching large-scale biomedical ontologies.ResultsExperimental results show that considering distinguishable matching clues in biomedical ontologies leads to a substantial improvement in all available information. Besides, incorporating different types of matchers with reliability results in a marked improvement, which is comparative to the state-of-the-art methods. The dominant matchers achieve F1 measures of 0.9271, 0.8218, and 0.5 on Anatomy, FMA-NCI (Foundation Model of Anatomy-National Cancer Institute), and FMA-SNOMED data sets, respectively. Extended reduction anchor is able to solve the scalability problem of matching large biomedical ontologies. It achieves a significant reduction in time complexity with little loss of F1 measure at the same time, with a 0.21% decrease on the Anatomy data set and 0.84% decrease on the FMA-NCI data set, but with a 2.65% increase on the FMA-SNOMED data set.ConclusionsThis paper systematically analyzes and compares the effectiveness of different matching clues, matchers, and combination strategies. Multiple empirical studies demonstrate that distinguishing clues have significant implications for matching biomedical ontologies. In contrast to the matchers with single clue, those combining multiple clues exhibit more stable and accurate performance. In addition, our results provide evidence that the approach based on extended reduction anchors performs well for large ontology matching tasks, demonstrating an effective solution for the problem.
| S-EPMC8414291 | biostudies-literature