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FC-NIRS: A Functional Connectivity Analysis Tool for Near-Infrared Spectroscopy Data. - BioMed research international
Functional near-infrared spectroscopy (fNIRS), a promising noninvasive imaging technique, has recently become an increasingly popular tool in resting-state brain functional connectivity (FC) studies. However, the corresponding software packages for FC analysis are still lacking. To facilitate fNIRS-based human functional connectome studies, we developed a MATLAB software package called "functional connectivity analysis tool for near-infrared spectroscopy data" (FC-NIRS). This package includes the main functions of fNIRS data preprocessing, quality control, FC calculation, and network analysis. Because this software has a friendly graphical user interface (GUI), FC-NIRS allows researchers to perform data analysis in an easy, flexible, and quick way. Furthermore, FC-NIRS can accomplish batch processing during data processing and analysis, thereby greatly reducing the time cost of addressing a large number of datasets. Extensive experimental results using real human brain imaging confirm the viability of the toolbox. This novel toolbox is expected to substantially facilitate fNIRS-data-based human functional connectome studies.
Dynamic functional connectivity revealed by resting-state functional near-infrared spectroscopy. - Biomedical optics express
The brain is a complex network with time-varying functional connectivity (FC) and network organization. However, it remains largely unknown whether resting-state fNIRS measurements can be used to characterize dynamic characteristics of intrinsic brain organization. In this study, for the first time, we used the whole-cortical fNIRS time series and a sliding-window correlation approach to demonstrate that fNIRS measurement can be ultimately used to quantify the dynamic characteristics of resting-state brain connectivity. Our results reveal that the fNIRS-derived FC is time-varying, and the variability strength (Q) is correlated negatively with the time-averaged, static FC. Furthermore, the Q values also show significant differences in connectivity between different spatial locations (e.g., intrahemispheric and homotopic connections). The findings are reproducible across both sliding-window lengths and different brain scanning sessions, suggesting that the dynamic characteristics in fNIRS-derived cerebral functional correlation results from true cerebral fluctuation.
Mesoscale eddies transport deep-sea sediments. - Scientific reports
Mesoscale eddies, which contribute to long-distance water mass transport and biogeochemical budget in the upper ocean, have recently been taken into assessment of the deep-sea hydrodynamic variability. However, how such eddies influence sediment movement in the deepwater environment has not been explored. Here for the first time we observed deep-sea sediment transport processes driven by mesoscale eddies in the northern South China Sea via a full-water column mooring system located at 2100 m water depth. Two southwestward propagating, deep-reaching anticyclonic eddies passed by the study site during January to March 2012 and November 2012 to January 2013, respectively. Our multiple moored instruments recorded simultaneous or lagging enhancement of suspended sediment concentration with full-water column velocity and temperature anomalies. We interpret these suspended sediments to have been trapped and transported from the southwest of Taiwan by the mesoscale eddies. The net near-bottom southwestward sediment transport by the two events is estimated up to one million tons. Our study highlights the significance of surface-generated mesoscale eddies on the deepwater sedimentary dynamic process.
Further support for the importance of the suppressive signal (pull) during the push-pull perceptual training. - Vision research
We previously designed a push-pull perceptual training protocol that effectively reduces sensory eye dominance (SED) and enhances binocular depth detection in human adults (Xu, He, & Ooi, 2010a). During the training, an attention cue precedes a pair of binocular competitive stimulus to induce dominance of the weak eye and suppression of the strong eye. To verify that the success of the protocol is due to the suppression of the signals evoked by the stimulus in the strong eye, rather than to the attention cueing per se, we employed two new push-pull training protocols that did not involve attention cueing. Instead, we used the specific configurations of the boundary contours of the binocular competitive stimulus to render the strong eye suppressed. The first, MBC push-pull protocol has a half-image with grating feature but no boundary contour in the strong eye. The second, BBC push-pull protocol has a half-image with both grating feature and boundary contour in the strong eye. For both protocols, the weak eye receives a half-image with strong grating feature and boundary contour. These boundary contour configurations ensure that the weak eye remains dominant while the strong eye is suppressed during training. Each observer was trained with both protocols at two parafoveal (2Â°) retinal locations. We found that both protocols significantly reduce SED and binocular depth threshold. This confirms the basis of the push-pull protocol is the suppression of the strong eye, rather than the attention cueing per se. We further found that the learning effect (SED reduction) is more effective in the BBC push-pull protocol where the suppressed half-image in the strong eye carries both grating feature and boundary contour information, than in the MBC push-pull protocol where the boundary contour information is absent from the strong eye's half-image. This suggests that the learning effect depends in part on the availability of the image attributes for processing (suppression) during the push-pull perceptual training.Copyright Â© 2012 Elsevier Ltd. All rights reserved.
A new nonlinear parameter in the developed strain-to-applied strain of the soft tissues and its application in ultrasound elasticity imaging. - Ultrasound in medicine & biology
Strain developed under quasi-static deformation has been mostly used in ultrasound elasticity imaging (UEI) to determine the stiffness change of tissues. However, the strain measure in UEI is often less sensitive to a subtle change of stiffness. This is particularly true for Crohn's disease where we have applied strain imaging to the differentiation of acutely inflamed bowel from chronically fibrotic bowel. In this study, a new nonlinear elastic parameter of the soft tissues is proposed to overcome this limit. The purpose of this study is to evaluate the newly proposed method and demonstrate its feasibility in the UEI. A nonlinear characteristic of soft tissues over a relatively large dynamic range of strain was investigated. A simplified tissue model based on a finite element (FE) analysis was integrated with a laboratory developed ultrasound radio-frequency (RF) signal synthesis program. Two-dimensional speckle tracking was applied to this model to simulate the nonlinear behavior of the strain developed in a target inclusion over the applied average strain to the surrounding tissues. A nonlinear empirical equation was formulated and optimized to best match the developed strain-to-applied strain relation obtained from the FE simulation. The proposed nonlinear equation was applied to in vivo measurements and nonlinear parameters were further empirically optimized. For an animal model, acute and chronic inflammatory bowel disease was induced in Lewis rats with trinitrobenzene sulfonic acid (TNBS)-ethanol treatments. After UEI, histopathology and direct mechanical measurements were performed on the excised tissues. The extracted nonlinear parameter from the developed strain-to-applied strain relation differentiated the three different tissue types with 1.96 Â± 0.12 for normal, 1.50 Â± 0.09 for the acutely inflamed and 1.03 Â± 0.08 for the chronically fibrotic tissue. T-tests determined that the nonlinear parameters between normal, acutely inflamed and fibrotic tissue types were statistically significantly different (normal/ fibrotic [p = 0.0000185], normal/acutely inflamed [p = 0.0013] and fibrotic/acutely inflamed [p = 0.0029]). This technique may provide a sensitive and robust tool to assess subtle stiffness changes in tissues such as in acutely inflamed bowel wall.Copyright Â© 2012 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.
A binocular perimetry study of the causes and implications of sensory eye dominance. - Vision research
Sensory eye dominance (SED) reflects an imbalance of interocular inhibition in the binocular network. Extending an earlier work (Ooi & He, 2001) that measured global SED within the central 6Â°, the current study measured SED locally at 17 locations within the central 8Â° of the binocular visual field. The eccentricities (radius) chosen for this, "binocular perimetry", study were 0Â° (fovea), 2Â° and 4Â°. At each eccentricity, eight concentric locations (polar angle: 0Â°, 45Â°, 90Â°, 135Â°, 180Â°, 225Â°, 270Â°, and 315Â°) were tested. The outcome, an SED map, sets up comparison between local SED and other visual functions [monocular contrast threshold, binocular disparity threshold, reaction time to detect depth, the dynamics of binocular rivalry and motor eye dominance]. Our analysis shows that an observer's SED varies gradually across the binocular visual field both in its sign and magnitude. The strong eye channel revealed in the SED measurement does not always have a lower monocular contrast threshold, and does not need to be the motor dominant eye. There exists significant correlation between SED and binocular disparity threshold, and between SED and the response time to detect depth of a random-dot stereogram. A significant correlation is also found between SED and the eye that predominates when viewing an extended duration binocular rivalry stimulus. While it is difficult to attribute casual factors based on correlation analyses, these observations agree with the notion that an imbalance of interocular inhibition, which is largely revealed as SED, is a significant factor impeding binocular visual perception.Copyright Â© 2011 Elsevier Ltd. All rights reserved.
Ultrasound elasticity imaging for detecting intestinal fibrosis and inflammation in rats and humans with Crohn's disease. - Gastroenterology
Intestinal fibrosis causes many complications of Crohn's disease (CD). Available biomarkers and imaging modalities lack sufficient accuracy to distinguish intestinal inflammation from fibrosis. Transcutaneous ultrasound elasticity imaging (UEI) is a promising, noninvasive approach for measuring tissue mechanical properties. We hypothesized that UEI could differentiate inflammatory from fibrotic bowel wall changes in both animal models of colitis and humans with CD.Female Lewis rats underwent weekly trinitrobenzene sulfonic acid enemas yielding models of acute inflammatory colitis (n = 5) and chronic intestinal fibrosis (n = 6). UEI scanning used a novel speckle-tracking algorithm to estimate tissue strain. Resected bowel segments were evaluated for evidence of inflammation and fibrosis. Seven consecutive patients with stenotic CD were studied with UEI and their resected stenotic and normal bowel segments were evaluated by ex vivo elastometry and histopathology.Transcutaneous UEI normalized strain was able to differentiate acutely inflamed (-2.07) versus chronic fibrotic (-1.10) colon in rat models of inflammatory bowel disease (IBD; P = .037). Transcutaneous UEI normalized strain also differentiated stenotic (-0.87) versus adjacent normal small bowel (-1.99) in human CD (P = .0008), and this measurement also correlated well with ex vivo elastometry (r = -0.81).UEI can differentiate inflammatory from fibrotic intestine in rat models of IBD and can differentiate between fibrotic and unaffected intestine in a pilot study in humans with CD. UEI represents a novel technology with potential to become a new objective measure of progression of intestinal fibrosis. Prospective clinical studies in CD are needed.Copyright Â© 2011 AGA Institute. Published by Elsevier Inc. All rights reserved.
Push-pull training reduces foveal sensory eye dominance within the early visual channels. - Vision research
A push-pull training protocol is applied to reduce sensory eye dominance in the foveal region. The training protocol consists of cueing the weak eye to force it to become dominant while the strong eye is suppressed when a pair of dichoptic orthogonal grating stimulus is subsequently presented to it (Ooi & He, 1999). We trained with four pairs of dichoptic orthogonal gratings (0Â°/90Â°, 90Â°/0Â°, 45Â°/135Â° and 135Â°/45Â° at 3cpd) to affect the interocular inhibitory interaction tuned to the four trained orientations (0Â°, 45Â°, 90Â° and 135Â°). After a 10-day training session, we found a significant learning effect (reduced sensory eye dominance) at the trained orientations as well as at two other untrained orientations (22.5Â° and 67.5Â°). This suggests that the four pairs of oriented training stimuli are sufficient to produce a learning effect at any other orientation. The nearly complete transfer of the learning effect across orientation is attributed to the fact that the trained and untrained orientations are close enough to fall in the same orientation tuning function of the early visual cortical neurons (âˆ¼37.5Â°). Applying the same notion of transfer of learning within the same feature channel, we also found a large transfer effect to an untrained spatial frequency (6cpd), which is 1 octave higher than the trained spatial frequency (3cpd). Furthermore, we found that stereopsis is improved, as is the competitive ability between the two eyes, after the push-pull training. Our data analysis suggests that these improvements are correlated with the reduced sensory eye dominance after the training, i.e., due to a more balanced interocular inhibition. We also found that the learning effect (reduced SED and stereo threshold) can be retained for more than a year after the termination of the push-pull training.Copyright Â© 2011 Elsevier Ltd. All rights reserved.
Perceptual learning to reduce sensory eye dominance beyond the focus of top-down visual attention. - Vision research
Perceptual learning is an important means for the brain to maintain its agility in a dynamic environment. Top-down focal attention, which selects task-relevant stimuli against competing ones in the background, is known to control and select what is learned in adults. Still unknown, is whether the adult brain is able to learn highly visible information beyond the focus of top-down attention. If it is, we should be able to reveal a purely stimulus-driven perceptual learning occurring in functions that are largely determined by the early cortical level, where top-down attention modulation is weak. Such an automatic, stimulus-driven learning mechanism is commonly assumed to operate only in the juvenile brain. We performed perceptual training to reduce sensory eye dominance (SED), a function that taps on the eye-of-origin information represented in the early visual cortex. Two retinal locations were simultaneously stimulated with suprathreshold, dichoptic orthogonal gratings. At each location, monocular cueing triggered perception of the grating images of the weak eye and suppression of the strong eye. Observers attended only to one location and performed orientation discrimination of the gratings seen by the weak eye, while ignoring the highly visible gratings at the second, unattended, location. We found SED was not only reduced at the attended location, but also at the unattended location. Furthermore, other untrained visual functions mediated by higher cortical levels improved. An automatic, stimulus-driven learning mechanism causes synaptic alterations in the early cortical level, with a far-reaching impact on the later cortical levels.Copyright Â© 2011 Elsevier Ltd. All rights reserved.
Retrieval of total suspended matter (TSM) and chlorophyll-a (Chl-a) concentration from remote-sensing data for drinking water resources. - Environmental monitoring and assessment
The concentrations of chlorophyll-a (Chl-a) and total suspended matter (TSM) are major water quality parameters that can be retrieved using remotely sensed data. Water sampling works were conducted on 15 July 2007 and 13 September 2008 concurrent with the Indian Remote-Sensing Satellite (IRS-P6) overpass of the Shitoukoumen Reservoir. Both empirical regression and back-propagation artificial neural network (ANN) models were established to estimate Chl-a and TSM concentration with both in situ and satellite-received radiances signals. It was found that empirical models performed well on the TSM concentration estimation with better accuracy (R (2)â€‰= 0.94, 0.91) than their performance on Chl-a concentration (R (2)â€‰= 0.62, 0.75) with IRS-P6 imagery data, and the models accuracy marginally improved with in situ spectra data. Our results indicated that the ANN model performed better for both Chl-a (R (2)â€‰= 0.91, 0.82) and TSM (R (2)â€‰= 0.98, 0.94) concentration estimation through in situ collected spectra; the same trend followed for IRS-P6 imagery data (R (2)â€‰= 0.75 and 0.90 for Chl-a; R (2)â€‰= 0.97 and 0.95 for TSM). The relative root mean square errors (RMSEs) from the empirical model for TSM (Chl-a) were less than 15% (respectively 27.2%) with both in situ and IRS-P6 imagery data, while the RMSEs were less than 7.5% (respectively 18.4%) from the ANN model. Future work still needs to be undertaken to derive the dynamic characteristic of Shitoukoumen Reservoir water quality with remotely sensed IRS-P6 or Landsat-TM data. The algorithms developed in this study will also need to be tested and refined with more imagery data acquisitions combined with in situ spectra data.
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