Development of grouped icEEG for the study of cognitive processing.
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ABSTRACT:
SUBMITTER: Kadipasaoglu CM
PROVIDER: S-EPMC4508923 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The Adolescent Brain Cognitive Development (ABCD) Study is an ongoing, nationwide study of the effects of environmental influences on behavioral and brain development in adolescents. The main objective of the study is to recruit and assess over eleven thousand 9-10-year-olds and follow them over the course of 10 years to characterize normative brain and cognitive development, the many factors that influence brain development, and the effects of those factors on mental health and other outcomes. The study employs state-of-the-art multimodal brain imaging, cognitive and clinical assessments, bioassays, and careful assessment of substance use, environment, psychopathological symptoms, and social functioning. The data is a resource of unprecedented scale and depth for studying typical and atypical development. The aim of this manuscript is to describe the baseline neuroimaging processing and subject-level analysis methods used by ABCD. Processing and analyses include modality-specific corrections for distortions and motion, brain segmentation and cortical surface reconstruction derived from structural magnetic resonance imaging (sMRI), analysis of brain microstructure using diffusion MRI (dMRI), task-related analysis of functional MRI (fMRI), and functional connectivity analysis of resting-state fMRI. This manuscript serves as a methodological reference for users of publicly shared neuroimaging data from the ABCD Study.
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Project description:Bidirectional reflectance distribution function (BRDF) effects are a persistent issue for the analysis of vegetation in airborne imaging spectroscopy data, especially when mosaicking results from adjacent flightlines. With the advent of large airborne imaging efforts from NASA and the U.S. National Ecological Observatory Network (NEON), there is increasing need for methods that are flexible and automatable across images with diverse land cover. Flexible bidirectional reflectance distribution function (FlexBRDF) is built upon the widely used kernel method, with additional features including stratified random sampling across flightline groups, dynamic land cover stratification by normalized difference vegetation index (NDVI), interpolation of correction coefficients across NDVI bins, and the use of a reference solar zenith angle. We demonstrate FlexBRDF using nine long (150-400 km) airborne visible/infrared imaging spectrometer (AVIRIS)-Classic flightlines collected on 22 May 2013 over Southern California, where diverse land cover and a wide range of solar illumination yield significant BRDF effects. We further test the approach on additional AVIRIS-Classic data from California, AVIRIS-Next Generation data from the Arctic and India, and NEON imagery from Wisconsin. Comparison of overlapping areas of flightlines show that models built from multiple flightlines performed better than those built for single images (root mean square error improved up to 2.3% and mean absolute deviation 2.5%). Standardization to a common solar zenith angle among a flightline group improved performance, and interpolation across bins minimized between-bin boundaries. While BRDF corrections for individual sites suffice for local studies, FlexBRDF is an open source option that is compatible with bulk processing of large airborne data sets covering diverse land cover needed for calibration/validation of forthcoming spaceborne imaging spectroscopy missions.
| S-EPMC9286663 | biostudies-literature
Project description:Highlights • Epidemic curves created by using an agent-based model are presented.• The network of interactions, and thus the possibility of infection, is modeled with the scale-free Barabasi-Albert model. Modifications based on whether these interactions belong to a particular group are proposed.• A simple model of passing an infection via a direct interaction is proposed.• The influence of the network creation method, division into different numbers of groups and different times of intervention is presented.• The results are shown for two cases: the well-known influenza virus and the recently reported COVID-19. Background and Objective The currently active COVID-19 pandemic has increased, among others, public interest in the computational techniques enabling the study of disease-spreading processes. Thus far, numerous approaches have been used to study the development of epidemics, with special attention paid to the identification of crucial elements that can strengthen or weaken the dynamics of the process. The main thread of this research is associated with the use of the ordinary differential equations method. There also exist several approaches based on the analysis of flows in the Cellular Automata (CA) approach. Methods In this paper, we propose a new approach to disease-spread modeling. We start by creating a network that reproduces contacts between individuals in a community. This assumption makes the presented model significantly different from the ones currently dominant in the field. It also changes the approach to the act of infection. Usually, some parameters that describe the rate of new infections by taking into account those infected in the previous time slot are considered. With our model, we can individualize this process, considering each contact individually. Results The typical output from calculations of a similar type are epidemic curves. In our model, except of presenting the average curves, we show the deviations or ranges for particular results obtained in different simulation runs, which usually lead to significantly different results. This observation is the effect of the probabilistic character of the infection process, which can impact, in different runs, individuals with different significance to the community. We can also easily present the effects of different types of intervention. The effects are studied for different methods used to create the graph representing a community, which can correspond to different social bonds. Conclusions We see the potential usefulness of the proposition in the detailed study of epidemic development for specific environments and communities. The ease of entering new parameters enables the analysis of several specific scenarios for different contagious diseases.
| S-EPMC7449887 | biostudies-literature
Project description:BackgroundTime- and dose-to-event phenotypes used in basic science and translational studies are commonly measured imprecisely or incompletely due to limitations of the experimental design or data collection schema. For example, drug-induced toxicities are not reported by the actual time or dose triggering the event, but rather are inferred from the cycle or dose to which the event is attributed. This exemplifies a prevalent type of imprecise measurement called grouped failure time, where times or doses are restricted to discrete increments. Failure to appropriately account for the grouped nature of the data, when present, may lead to biased analyses.ResultsWe present groupedSurv, an R package which implements a statistically rigorous and computationally efficient approach for conducting genome-wide analyses based on grouped failure time phenotypes. Our approach accommodates adjustments for baseline covariates, and analysis at the variant or gene level. We illustrate the statistical properties of the approach and computational performance of the package by simulation. We present the results of a reanalysis of a published genome-wide study to identify common germline variants associated with the risk of taxane-induced peripheral neuropathy in breast cancer patients.ConclusionsgroupedSurv enables fast and rigorous genome-wide analysis on the basis of grouped failure time phenotypes at the variant, gene or pathway level. The package is freely available under a public license through the Comprehensive R Archive Network.
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Project description:Neuroimaging studies suggest that category-selective regions in higher-order visual cortex are topologically organized around specific anatomical landmarks: the mid-fusiform sulcus (MFS) in the ventral temporal cortex (VTC) and lateral occipital sulcus (LOS) in the lateral occipital cortex (LOC). To derive precise structure-function maps from direct neural signals, we collected intracranial EEG (icEEG) recordings in a large human cohort (n = 26) undergoing implantation of subdural electrodes. A surface-based approach to grouped icEEG analysis was used to overcome challenges from sparse electrode coverage within subjects and variable cortical anatomy across subjects. The topology of category-selectivity in bilateral VTC and LOC was assessed for five classes of visual stimuli-faces, animate non-face (animals/body-parts), places, tools, and words-using correlational and linear mixed effects analyses. In the LOC, selectivity for living (faces and animate non-face) and non-living (places and tools) classes was arranged in a ventral-to-dorsal axis along the LOS. In the VTC, selectivity for living and non-living stimuli was arranged in a latero-medial axis along the MFS. Written word-selectivity was reliably localized to the intersection of the left MFS and the occipito-temporal sulcus. These findings provide direct electrophysiological evidence for topological information structuring of functional representations within higher-order visual cortex.
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Project description:BACKGROUND: Motivational and cognitive abnormalities are frequently reported in pathological gambling. However, studies simultaneously investigating motivational and cognitive processing in problematic gamblers are lacking, limiting our understanding of the interplay between these systems in problematic gambling. Studies in non-clinical samples indicate that interactions between dorsal "executive" and ventral "affective" processing systems are necessary for adequate responses in various emotive situations. METHODS: We conducted a generalized Psycho-Physiological Interaction (gPPI) analysis to assess the influence of affective stimuli on changes in functional connectivity associated with response inhibition in 16 treatment seeking problematic gamblers (PRGs) and 15 healthy controls (HCs) using an affective Go-NoGo fMRI paradigm including neutral, gambling-related, positive and negative pictures as neutral and affective conditions. RESULTS: Across groups, task performance accuracy during neutral inhibition trials was positively correlated with functional connectivity between the left caudate and the right middle frontal cortex. During inhibition in the gambling condition, only in PRGs accuracy of task performance was positively correlated with functional connectivity within sub-regions of the dorsal executive system. Group interactions showed that during neutral inhibition, HCs exhibited greater functional connectivity between the left caudate and occipital cortex than PRGs. In contrast, during inhibition in the positive condition, PRGs compared to HCs showed greater functional connectivity between the left caudate and occipital cortex. During inhibition trials in the negative condition, a stronger functional connectivity between the left caudate and the right anterior cingulate cortex in PRGs compared to HCs was present. There were no group interactions during inhibition in the gambling condition. CONCLUSIONS: During gamble inhibition PRGs seem to benefit more from functional connectivity within the dorsal executive system than HCs, because task accuracy in this condition in PRGs is positively correlated with functional connectivity, although the groups show similar connectivity patterns during gamble inhibition. Greater functional connectivity between the ventral affective system and the dorsal executive system in PRGs in the affective conditions compared to HCs, suggests facilitation of the dorsal executive system when affective stimuli are present specifically in PRGs.
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Project description:The Adolescent Brain Cognitive Development (ABCD) Study is the largest single-cohort prospective longitudinal study of neurodevelopment and children's health in the United States. A cohort of n = 11,880 children aged 9-10 years (and their parents/guardians) were recruited across 22 sites and are being followed with in-person visits on an annual basis for at least 10 years. The study approximates the US population on several key sociodemographic variables, including sex, race, ethnicity, household income, and parental education. Data collected include assessments of health, mental health, substance use, culture and environment and neurocognition, as well as geocoded exposures, structural and functional magnetic resonance imaging (MRI), and whole-genome genotyping. Here, we describe the ABCD Study aims and design, as well as issues surrounding estimation of meaningful associations using its data, including population inferences, hypothesis testing, power and precision, control of covariates, interpretation of associations, and recommended best practices for reproducible research, analytical procedures and reporting of results.
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Project description:We investigated coordinated movements between the eyes and head ("eye-head coordination") in relation to vision for action. Several studies have measured eye and head movements during a single gaze shift, focusing on the mechanisms of motor control during eye-head coordination. However, in everyday life, gaze shifts occur sequentially and are accompanied by movements of the head and body. Under such conditions, visual cognitive processing influences eye movements and might also influence eye-head coordination because sequential gaze shifts include cycles of visual processing (fixation) and data acquisition (gaze shifts). In the present study, we examined how the eyes and head move in coordination during visual search in a large visual field. Subjects moved their eyes, head, and body without restriction inside a 360° visual display system. We found patterns of eye-head coordination that differed those observed in single gaze-shift studies. First, we frequently observed multiple saccades during one continuous head movement, and the contribution of head movement to gaze shifts increased as the number of saccades increased. This relationship between head movements and sequential gaze shifts suggests eye-head coordination over several saccade-fixation sequences; this could be related to cognitive processing because saccade-fixation cycles are the result of visual cognitive processing. Second, distribution bias of eye position during gaze fixation was highly correlated with head orientation. The distribution peak of eye position was biased in the same direction as head orientation. This influence of head orientation suggests that eye-head coordination is involved in gaze fixation, when the visual system processes retinal information. This further supports the role of eye-head coordination in visual cognitive processing.
| S-EPMC4370616 | biostudies-literature