Longitudinal white-matter abnormalities in sports-related concussion: A diffusion MRI study

Objective To study longitudinal recovery trajectories of white matter after sports-related concussion (SRC) by performing diffusion tensor imaging (DTI) on collegiate athletes who sustained SRC. Methods Collegiate athletes (n = 219, 82 concussed athletes, 68 contact-sport controls, and 69 non–contact-sport controls) were included from the Concussion Assessment, Research and Education Consortium. The participants completed clinical assessments and DTI at 4 time points: 24 to 48 hours after injury, asymptomatic state, 7 days after return-to-play, and 6 months after injury. Tract-based spatial statistics was used to investigate group differences in DTI metrics and to identify white-matter areas with persistent abnormalities. Generalized linear mixed models were used to study longitudinal changes and associations between outcome measures and DTI metrics. Cox proportional hazards model was used to study effects of white-matter abnormalities on recovery time. Results In the white matter of concussed athletes, DTI-derived mean diffusivity was significantly higher than in the controls at 24 to 48 hours after injury and beyond the point when the concussed athletes became asymptomatic. While the extent of affected white matter decreased over time, part of the corpus callosum had persistent group differences across all the time points. Furthermore, greater elevation of mean diffusivity at acute concussion was associated with worse clinical outcome measures (i.e., Brief Symptom Inventory scores and symptom severity scores) and prolonged recovery time. No significant differences in DTI metrics were observed between the contact-sport and non–contact-sport controls. Conclusions Changes in white matter were evident after SRC at 6 months after injury but were not observed in contact-sport exposure. Furthermore, the persistent white-matter abnormalities were associated with clinical outcomes and delayed recovery tim

Optimizing Preprocessing and Analysis Pipelines for Single-Subject fMRI: 2. Interactions with ICA, PCA, Task Contrast and Inter-Subject Heterogeneity

A variety of preprocessing techniques are available to correct subject-dependant artifacts in fMRI, caused by head motion and physiological noise. Although it has been established that the chosen preprocessing steps (or “pipeline”) may significantly affect fMRI results, it is not well understood how preprocessing choices interact with other parts of the fMRI experimental design. In this study, we examine how two experimental factors interact with preprocessing: between-subject heterogeneity, and strength of task contrast. Two levels of cognitive contrast were examined in an fMRI adaptation of the Trail-Making Test, with data from young, healthy adults. The importance of standard preprocessing with motion correction, physiological noise correction, motion parameter regression and temporal detrending were examined for the two task contrasts. We also tested subspace estimation using Principal Component Analysis (PCA), and Independent Component Analysis (ICA). Results were obtained for Penalized Discriminant Analysis, and model performance quantified with reproducibility (R) and prediction metrics (P). Simulation methods were also used to test for potential biases from individual-subject optimization. Our results demonstrate that (1) individual pipeline optimization is not significantly more biased than fixed preprocessing. In addition, (2) when applying a fixed pipeline across all subjects, the task contrast significantly affects pipeline performance; in particular, the effects of PCA and ICA models vary with contrast, and are not by themselves optimal preprocessing steps. Also, (3) selecting the optimal pipeline for each subject improves within-subject (P,R) and between-subject overlap, with the weaker cognitive contrast being more sensitive to pipeline optimization. These results demonstrate that sensitivity of fMRI results is influenced not only by preprocessing choices, but also by interactions with other experimental design factors. This paper outlines a quantitative procedure to denoise data that would otherwise be discarded due to artifact; this is particularly relevant for weak signal contrasts in single-subject, small-sample and clinical datasets

An open science resource for establishing reliability and reproducibility in functional connectomics

Efforts to identify meaningful functional imaging-based biomarkers are limited by the ability to reliably characterize inter-individual differences in human brain function. Although a growing number of connectomics-based measures are reported to have moderate to high test-retest reliability, the variability in data acquisition, experimental designs, and analytic methods precludes the ability to generalize results. The Consortium for Reliability and Reproducibility (CoRR) is working to address this challenge and establish test-retest reliability as a minimum standard for methods development in functional connectomics. Specifically, CoRR has aggregated 1,629 typical individuals’ resting state fMRI (rfMRI) data (5,093 rfMRI scans) from 18 international sites, and is openly sharing them via the International Data-sharing Neuroimaging Initiative (INDI). To allow researchers to generate various estimates of reliability and reproducibility, a variety of data acquisition procedures and experimental designs are included. Similarly, to enable users to assess the impact of commonly encountered artifacts (for example, motion) on characterizations of inter-individual variation, datasets of varying quality are included

PH Control of Monoraphidium Minutum Grown in a Batch Culture Environment

Research at the National Renewable Energy Laboratory (NREL) is being conducted to develop low-cost technology for coupling the exhaust from fossil fuel-fired power plants to the growth of microalgae for the dual purpose of recycling carbon dioxide emissions and producing a renewable fuel source. Microalgae are unicellular photosynthesizers with tremendous potential for rapid division (growth) and high lipid production. The carbon assimilated into lipids provides a renewable source for biodiesel fuel. Experiments are being conducted to explore the growth rates of microalgae exposed to simulated flue gas. Interest is focused on the effectiveness of pH control for regulating gas dosage to optimize cell growth. Preliminary results using the species, Monoraphidium minutum, indicate no advantage to this method

MRI brain templates of the male Yucatan minipig

The pig is growing in popularity as an experimental animal because its gyrencephalic brain is similar to humans. Currently, however, there is a lack of appropriate brain templates to support functional and structural neuroimaging pipelines. The primary contribution of this work is an average volume from an iterative, non-linear registration of 70 five- to seven-month-old male Yucatan minipigs. In addition, several aspects of this study are unique, including the comparison of linear and non-linear template generation, the characterization of a large and homogeneous cohort, an analysis of effective resolution after averaging, and the evaluation of potential in-template bias as well as a comparison with a template from another minipig species using a “left-out” validation set. We found that within our highly homogeneous cohort, non-linear registration produced better templates, but only marginally so. Although our T1-weighted data were resolution limited, we preserved effective resolution across the multi-subject average, produced templates that have high gray-white matter contrast and demonstrate superior registration accuracy compared to an alternative minipig template

Generalized RAICAR: Discover homogeneous subject (sub)groups by reproducibility of their intrinsic connectivity networks

Existing spatial independent component analysis (ICA) methods for multi-subject fMRI datasets have mainly focused on detecting common components across subjects, under the assumption that all the subjects in a group share the same (identical) components. However, as a data-driven approach, ICA could potentially serve as an exploratory tool at multi-subject level, and help us uncover inter-subject differences in patterns of connectivity (e.g., find subtypes in patient populations). In this work, we propose a methodology named gRAICAR that exploits the data-driven nature of ICA to allow discovery of sub-groupings of subjects based on reproducibility of their ICA components. This technique allows us not only to find highly reproducible common components across subjects but also to explore (without a priori subject groupings) components that could classify all subjects into sub-groups. gRAICAR generalizes the reproducibility framework previously developed for single subjects (Ranking and averaging independent component analysis by reproducibility-RAICAR-Yang et al., Hum Brain Mapp, 2008) to multiple-subject analysis. For each group-level component, gRAICAR generates its reproducibility matrix and further computes two metrics, inter-subject consistency and intra-subject reliability, to characterize inter-subject variability and reflect contributions from individual subjects. Nonparametric tests are employed to examine the significance of both the inter-subject consistency and the separation of subject groups reflected in the component. Our validations based on simulated and experimental resting-state fMRI datasets demonstrated the advantage of gRAICAR in extracting features reflecting potential subject groupings. It may facilitate discovery of the underlying brain functional networks with substantial potential to inform our understandings of development, neurodegenerative conditions, and psychiatric disorders. (C) 2012 Elsevier Inc. All rights reserved