checkerboard pattern
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BACKGROUND: One possible approach how to economically facilitate gene expression profiling is to use the L1000 platform which measures the expression of ∼1,000 landmark genes and uses a computational method to infer the expression of another ∼10,000 genes. One such method for the gene expression inference is a D-GEX which employs neural networks. RESULTS: We propose two novel D-GEX architectures that significantly improve the quality of the inference by increasing the capacity of a network without any increase in the number of trained parameters. The architectures partition the network into individual towers. Our best proposed architecture - a checkerboard architecture with a skip connection and five towers - together with minor changes in the training protocol improves the average mean absolute error of the inference from 0.134 to 0.128. CONCLUSIONS: Our proposed approach increases the gene expression inference accuracy without increasing the number of weights of the model and thus without increasing the memory footprint of the model that is limiting its usage.
- Klíčová slova
- Checkerboard architecture, Gene expression, Neural network, Tower architecture,
- MeSH
- algoritmy MeSH
- exprese genu MeSH
- genové regulační sítě MeSH
- neuronové sítě * MeSH
- stanovení celkové genové exprese * MeSH
- Publikační typ
- časopisecké články MeSH
- MeSH
- adaptace na tmu MeSH
- dospělí MeSH
- elektrofyziologie MeSH
- evokované potenciály MeSH
- lidé MeSH
- percepce velikosti MeSH
- světelná stimulace MeSH
- zraková percepce * MeSH
- zraková pole MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
The assembly of local communities from regional species pools is shaped by historical aspects of distribution, environmental conditions, and biotic interactions. We studied local community assembly patterns in African annual killifishes of the genus Nothobranchius (Cyprinodontiformes), investigating data from 168 communities across the entire range of regionally co-existing species. Nothobranchius are small fishes associated with annually desiccating pools. We detected a nested pattern of local communities in one region (Southern Mozambique, with Nothobranchius furzeri as the core and dominant species), but no nestedness was found in the second region (Central Mozambique, with Nothobranchius orthonotus being the dominant species). A checkerboard pattern of local Nothobranchius community assembly was demonstrated in both regions. Multivariate environmental niche modeling revealed moderate differences in environmental niche occupancy between three monophyletic clades that largely co-occurred geographically and greater differences between strictly allopatric species within the clades. Most variation among species was observed along an altitudinal gradient; N. furzeri and Nothobranchius kadleci were absent from coastal plains, Nothobranchius pienaari, Nothobranchius rachovii, and Nothobranchius krysanovi were associated with lower altitude and N. orthonotus was intermediate and geographically most widespread species. We discuss implications for ecological and evolutionary research in this taxon.
- Klíčová slova
- Africa, altitudinal gradient, checkerboard pattern, dispersal, ephemeral pools, temporary water body,
- Publikační typ
- časopisecké články MeSH
This study deals with the effect of stimulus contrast, between 1.3% and 96%, on the visual evoked potentials (VEPs) for onset of motion and for pattern reversal of checkerboard stimuli. The VEPs for pattern reversal and for the onset of motion both contain an initial positive peak (P1; peak latency about 120 msec) followed by a later negative peak (N2; peak latency 160-200 msec). However the P1 peak dominates the pattern-reversal VEP when recorded from the midline occipital lead, where it is maximal, while the N2 peak is larger in the motion-onset VEP, especially when recorded from unipolar lateral occipital leads. Whereas the amplitude of the P1 peak in both the pattern-reversal VEP and the motion-onset VEP decreases with decreasing contrast (becoming undetectable at a contrast of about 2% for the motion-onset VEP), the amplitude of the N2 peak in both types of VEP does not vary significantly with contrast, above a contrast of 1.3%. The increase in peak latency with decreasing contrast is also more pronounced for the positive than the negative peaks of both types of VEP. Taking into account the high contrast sensitivity of the magnocellular system (thought to be involved in the processing of motion) compared with the parvocellular system (probably more concerned with the processing of form), our findings suggest that for both motion-onset and pattern-reversal VEPs the negative peak is attributable to the motion-processing magnocellular pathway and the positive peak to the form-processing parvocellular system.
- MeSH
- časové faktory MeSH
- citlivost na kontrast fyziologie MeSH
- dospělí MeSH
- lidé MeSH
- oční fixace MeSH
- rozpoznávání obrazu fyziologie MeSH
- vnímání pohybu fyziologie MeSH
- zrakové evokované potenciály fyziologie MeSH
- zrakové korové centrum fyziologie MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
PURPOSE: To describe the effect of dioptric blur on visual evoked potentials (VEPs) induced by motion onset (MO-VEPs). METHODS: The effect of dioptric blur up to 4 D on MO-VEPs was tested on 12 subjects using central, peripheral, and full-field stimulation with a low-contrast structure of concentric circles with spatial frequency <1 c/°. The results were compared to VEPs evoked by 15' and 60' checkerboard pattern-reversal (PR-VEPs). The relationship between peak time and interpeak amplitude of the dominant components was related to the level of dioptric blur using linear regression. RESULTS: The MO-VEPs did not show a significant peak prolongation (P > 0.28) or amplitude attenuation (P > 0.14) with the blur, whereas for the PR-VEPs we observed a significant decrease in amplitude (P < 0.001) and increase in peak time (P < 0.001) for both checkerboard sizes. CONCLUSIONS: For MO-VEPs induced by radial motion of low contrast and low spatial frequency pattern, the change in retinal blur does not affect the peak time or the interpeak amplitude of the dominant N2 component. TRANSLATIONAL RELEVANCE: The resistance to retinal blur that we demonstrated for MO-VEP provides a diagnostic opportunity to test the integrity of the visual system and reveal a retrobulbar impairment even in uncorrected refractive errors.
- MeSH
- lidé MeSH
- zrakové evokované potenciály * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
A rapid checkerboard pattern change is used to elicit pattern-reversal visual evoked potentials (PR VEPs). CRT or LCD monitors do not allow immediate reversal of the entire pattern. The study aimed to construct a new stimulator whose characteristics approximate an instantaneous reversal and verify whether the improvement is reflected in PR VEPs. A new stimulator using a matrix of 12 × 48 independent white square LEDs was designed and compared with LCDs and CRTs. The effect on the PR VEP peak times and amplitudes of N70, P100, and P140 waves was evaluated in ten subjects. The LED stimulator showed significantly better performance in the rate of change of illuminance, change of pattern, luminance settling and stability. The PR VEP amplitudes of N75, P100, and N140 did not show significant differences. The sum of interpeak amplitudes was significantly larger for the LCD than for the other monitors. The peak times of the waves evoked by the LED were shorter than those evoked by the LCD and CRT for the N75 wave and a check size of 30´. LED stimulators are a better alternative to CRTs for PR VEPs than current LCDs. LEDs also seem to be better than CRTs, but further research is necessary to obtain significant results.
- Publikační typ
- časopisecké články MeSH
Motion-onset visual evoked potentials (MO VEPs) are robust to dioptric blur when low contrast and low spatial frequency patterns are used for stimulation. To reveal mechanisms of MO VEPs robustness, we studied whether the resistance to defocus persists even when using a high-contrast checkerboard using digital defocus in the emmetropic eyes of 13 subjects (males 20-60 years). We compared the dominant components of MO VEPs to pattern-reversal VEPs (PR VEP), which are sensitive to the blur. For stimulation, we used checkerboard patterns with 15´ and 60´ checks. To defocus the checkerboard, we rendered it with a second-order Zernike polynomial ( Z 2 0 ) with an equivalent defocus of 0, 2, or 4 D. For PR VEP, the checkerboards were reversed in terms of their contrast. To evoke MO VEP, the checkerboard of 60´ checks moved for 200 ms with a speed of 5 or 10 deg/s in the cardinal directions. The MO VEP did not change in peak time (P ≥ 0.0747) or interpeak amplitude (P > 0.0772) with digital blur. In contrast, for PR VEP, the results showed a decrease in interpeak amplitude (P ≤ 6.65ˑ10-4) and an increase in peak time (P ≤ 0.0385). Thus, we demonstrated that MO VEPs evoked by checkerboard, structure containing high spatial content, can be robust to defocus.
- Klíčová slova
- Digital blur, Motion-onset, Pattern-reversal, Visual evoked potential,
- MeSH
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- světelná stimulace MeSH
- vnímání pohybu fyziologie MeSH
- zrakové evokované potenciály * fyziologie MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
The greatest threat and medicinal impact within gram-positive pathogens are posed by two bacterial genera, Staphylococcus and Enterococcus. Chalcones have a wide range of biological activities and are recognized as effective templates in medicinal chemistry. This study provides comprehensive insight into the anti-staphylococcal and anti-enterococcal activities of two recently published brominated and chlorinated pyrazine-based chalcones, CH-0y and CH-0w. Their effects against 4 reference and 12 staphylococcal and enterococcal clinical isolates were evaluated. Bactericidal action, the activity in combination with selected conventional antibiotics, the study of post-antimicrobial effect (PAE, PAE/SME), and in vitro and in vivo toxicity, were included. In CH-0y, anti-staphylococcal activity ranging from MIC = 15.625 to 62.5 μM, and activity against E. faecium from 31.25 to 62.5 μM was determined. In CH-0w, anti-staphylococcal activity ranging from 31.25 to 125 μM, and activity against E. faecium and E. faecalis (62.5 μM) was revealed. Both CH-0y and CH-0w showed bactericidal action, beneficial impact on bacterial growth delay within PAE and PAE/SME studies, and non/low toxicity in vivo. Compared to CH-0w, CH-0y seems to have higher anti-staphylococcal and less toxic potential. In conclusion, chalcones CH-0y and CH-0w could be considered as structural pattern for future adjuvants to selected antibiotic drugs.
Differences in visual evoked responses (VER) to three types of stimuli were studied in 70 volunteers, using checkerboard pattern reversal stimulation--a circular target in the central part of the visual field (VF) and stimuli composed of either the upper or the lower half of the circle. The responses to semicircular stimulation displayed great variability (latency shifts, reverse polarity, absence of a response), particularly to the upper half of the circle, where the amplitude of the responses was significantly smaller and their latency longer than in lower semicircle and whole circle stimulation.
- MeSH
- dospělí MeSH
- lidé MeSH
- oči - fyziologické jevy * MeSH
- zraková pole * MeSH
- zrakové evokované potenciály * MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Chronic glaucoma has been shown preferentially to damage larger retinal cells and optic nerve fibres that provide the input to the magnocellular visual pathway. We compared the motion-onset visual evoked potentials (primarily the magnocellular system) with those to standard pattern reversal in 20 patients with bilateral chronic glaucoma. For motion-onset visual evoked potentials, the pattern (isolated 40' checks of 10% contrast) moved in four cardinal directions (varied randomly from trial to trial) at a velocity of 10 deg/s for 20 ms, with an interstimulus interval of 1 s. In pattern-reversal stimulation, the checkerboard reversed at a rate of 2 reversals per second. In 60% of the eyes investigated, the results of both types of visual evoked potentials correlated, showing either normal (27.5%) or increased (32.5%) latencies. In the remaining 40% of the eyes, the normal pattern-reversal visual evoked potential latencies were accompanied by prolonged motion-onset visual evoked potentials. The high occurrence of delayed motion-onset visual evoked potentials in our patients confirms the primary magnocellular loss in chronic glaucoma and suggests that the motion-onset VEPs are suitable for detection of glaucomatous changes.
- MeSH
- chronická nemoc MeSH
- discus nervi optici patologie patofyziologie MeSH
- dospělí MeSH
- glaukom diagnóza patofyziologie MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- senioři MeSH
- testy zrakového pole MeSH
- vnímání barev fyziologie MeSH
- vnímání pohybu fyziologie MeSH
- zraková ostrost MeSH
- zraková pole MeSH
- zrakové dráhy fyziologie MeSH
- zrakové evokované potenciály fyziologie MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladiství MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
