The Past, Present, and Future of the Brain Imaging Data Structure (BIDS)

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS.

When shapes are more than shapes: perceptual, developmental, and neurophysiological basis for attributions of animacy and theory of mind

Among a variety of entities in their environment, what do humans consider alive or animate and how does this attribution of animacy promote development of more abstract levels of mentalizing? By decontextualizing the environment of bodily features, we review how physical movements give rise to perceived animacy in Heider-Simmel style animations. We discuss the developmental course of how perceived animacy shapes our interpretation of the social world, and specifically discuss when and how children transition from perceiving actions as goal-directed to attributing behaviors to unobservable mental states. This transition from a teleological stance, asserting a goal-oriented interpretation to an agent's actions, to a mentalistic stance allows older children to reason about more complex actions guided by hidden beliefs. The acquisition of these more complex cognitive behaviors happens developmentally at the same time neural systems for social cognition are coming online in young children. We review perceptual, developmental, and neural evidence to identify the joint cognitive and neural changes associated with when children begin to mentalize and how this ability is instantiated in the brain.

The PyMVPA BIDS-App: a robust multivariate pattern analysis pipeline for fMRI data

With the advent of multivariate pattern analysis (MVPA) as an important analytic approach to fMRI, new insights into the functional organization of the brain have emerged. Several software packages have been developed to perform MVPA analysis, but deploying them comes with the cost of adjusting data to individual idiosyncrasies associated with each package. Here we describe PyMVPA BIDS-App, a fast and robust pipeline based on the data organization of the BIDS standard that performs multivariate analyses using powerful functionality of PyMVPA. The app runs flexibly with blocked and event-related fMRI experimental designs, is capable of performing classification as well as representational similarity analysis, and works both within regions of interest or on the whole brain through searchlights. In addition, the app accepts as input both volumetric and surface-based data. Inspections into the intermediate stages of the analyses are available and the readability of final results are facilitated through visualizations. The PyMVPA BIDS-App is designed to be accessible to novice users, while also offering more control to experts through command-line arguments in a highly reproducible environment.

Acute effect of nut consumption on plasma total polyphenols, antioxidant capacity and lipid peroxidation

BACKGROUND

Nuts have been shown to have beneficial effects on human health due to the healthy fat content; however, the effect of antioxidants (i.e. polyphenols) in nuts have not been fully investigated. The present study aimed to assess the immediate effect of a polyphenol-rich meal (75% of energy from nuts: walnuts or almonds) and a polyphenol-free meal on plasma polyphenol content, antioxidant capacity and lipid peroxidation in healthy volunteers.

METHODS

Thirteen subjects participated in a randomized, crossover, intervention study. After an overnight fast, walnuts, almonds or a control meal in the form of smoothies were consumed by study subjects. Each subject participated on three occasions, 1 week apart, consuming one of the smoothies each time. Blood samples were obtained at fasting and then at intervals up to 3.5 h after consumption of the smoothies.

RESULTS

There was a significant increase in plasma polyphenol concentration following both nut meals, with peak concentrations being achieved at 90 min, and with a walnut meal having a more sustained higher concentration than an almond meal. The plasma total antioxidant capacity reached its highest point at 150 min postconsumption of the nut meals, and was higher after the almond compared to walnut meal. A gradual significant (P < 0.05) reduction in the susceptibility of plasma to lipid peroxidation was observed 90 min after ingestion of the nut meals. No changes were observed following consumption of control meal.

CONCLUSIONS

Consumption of both nuts increased plasma polyphenol concentrations, increased the total antioxidant capacity and reduced plasma lipid peroxidation.

Acute effect of nut consumption on plasma total polyphenols, antioxidant capacity and lipid peroxidation

BACKGROUND

Nuts have been shown to have beneficial effects on human health due to the healthy fat content; however, the effect of antioxidants (i.e. polyphenols) in nuts have not been fully investigated. The present study aimed to assess the immediate effect of a polyphenol-rich meal (75% of energy from nuts: walnuts or almonds) and a polyphenol-free meal on plasma polyphenol content, antioxidant capacity and lipid peroxidation in healthy volunteers.

METHODS

Thirteen subjects participated in a randomized, crossover, intervention study. After an overnight fast, walnuts, almonds or a control meal in the form of smoothies were consumed by study subjects. Each subject participated on three occasions, 1 week apart, consuming one of the smoothies each time. Blood samples were obtained at fasting and then at intervals up to 3.5 h after consumption of the smoothies.

RESULTS

There was a significant increase in plasma polyphenol concentration following both nut meals, with peak concentrations being achieved at 90 min, and with a walnut meal having a more sustained higher concentration than an almond meal. The plasma total antioxidant capacity reached its highest point at 150 min postconsumption of the nut meals, and was higher after the almond compared to walnut meal. A gradual significant (P < 0.05) reduction in the susceptibility of plasma to lipid peroxidation was observed 90 min after ingestion of the nut meals. No changes were observed following consumption of control meal.

CONCLUSIONS

Consumption of both nuts increased plasma polyphenol concentrations, increased the total antioxidant capacity and reduced plasma lipid peroxidation.

NCOA3: A molecular prognostic marker for melanoma

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Background: Nuclear receptor coactivator-3 (NCOA3, also known as AIB1 or SRC-3), a member of the steroid receptor coactivator 1 family, has been shown to be amplified in human breast cancer. We recently identified NCOA3 as differentially expressed in metastatic melanomas by gene expression profiling, suggesting its role as a possible molecular prognostic factor. In this study, we assessed the prognostic significance of NCOA3 expression in a large melanoma patient cohort using tissue micro-arrays (TMAs). Methods: We used a commercially available antibody against NCOA3 to perform immunohistochemical analysis of NCOA3 expression in TMAs containing primary melanoma specimens from 353 patients seen at the UCSF Melanoma Center. Cases included clinicopathologic information (e.g., age, sex, tumor location, tumor thickness, Clark level and ulceration), as well as sentinel lymph node (SLN) status, and information regarding relapse-free (RFS) and disease-specific (DSS) survival. NCOA3 expression was assessed on a 4-point scale (0–3) by an observer blinded to patient outcomes. Results: High NCOA3 expression was significantly predictive of SLN metastasis by univariate logistic regression (p=0.015), and associated with a higher mean positive SLN count (p=0.03, Le test). Kaplan-Meier analysis demonstrated a significant association between increased NCOA3 expression and reduced RFS as well as DSS (p=0.024, and p=0.031 by log-rank test, respectively). Multivariate step-wise logistic regression analysis of 12 factors revealed NCOA3 expression, along with tumor thickness, age, vascular involvement, and Clark level to be independent predictors of SLN status. Multivariate Cox regression analysis showed the independent impact of NCOA3 expression on RFS and DSS with the inclusion of the AJCC factors tumor thickness, ulceration, Clark level, tumor location, patient age and sex. Conclusions: These results reveal NCOA3 to be a novel, independent marker of melanoma outcome, with a significant impact on SLN metastasis, RFS and DSS.

No significant financial relationships to disclose.

Surface keratopathy after penetrating keratoplasty

PURPOSE

To determine the type and prevalence of epithelial abnormalities in the intermediate postoperative period after penetrating keratoplasty and to define the donor and recipient variables that influence the status of the graft epithelium.

DESIGN

Prospective cohort study.

METHODS

We prospectively followed the clinical course of 80 patients after penetrating keratoplasty. We monitored the status of the corneal epithelium for 3 months after surgery using slit-lamp biomicroscopy and fluorescein staining of the epithelium. Donor characteristics, recipient preoperative and postoperative variables, and postoperative medications were recorded. Epithelial abnormalities were analyzed against these variables by using univariate and combined statistical models to determine the impact of each variable on postoperative epithelial pathology. Main outcome measures included punctate keratopathy, macro-epithelial defects, hurricane keratopathy, rim defects, and filamentary keratopathy.

RESULTS

Sixty-three percent of all patient visits demonstrated punctate epithelial keratopathy (PEK). Hurricane keratopathy (51%) and filamentary keratopathy (14%) constituted the next most commonly observed abnormalities. Older recipient age and the use of topical antibiotics were associated with a higher prevalence of punctate epithelial keratopathy. The odds ratio (OR) for a 1-year increase in age is 1.0276 (95% CI, 1.1013-1.0442), and the OR for using topical antibiotics is 6.9028 (95% CI, 3.1506-15.1239). Use of topical ofloxacin and increased time after surgery were associated with lower prevalence of punctate keratopathy; ORs were 0.9806 (95% CI, 0.9736-0.9876) and 0.3662 (95% CI, 0.1688-0.7943), respectively. Decreased corneal sensation and the presence of anterior blepharitis preoperatively were associated with an increase in hurricane keratopathy; ORs were 8.8265 (CI, 2.3837-32.6835) and 3.2815 (CI, 1.7388-6.1931), respectively. Total storage time for the donor material was also associated with an increased prevalence of hurricane keratopathy (OR, 1.0316; CI, 1.0052-1.0220). Patients with rim defects and macro-epithelial defects were more likely to have antibiotic and topical lubrication prescribed. No specific variable was found to have a significant association with filamentary keratopathy, except possibly for death-to-preservation time, which had a P value of .0587.

CONCLUSIONS

Surface keratopathy is one of the most common complications of keratoplasty. Our study demonstrates that older age, preoperative lid disease, and decreased preoperative corneal sensation appear to increase the probability of clinically significant epithelial surface abnormalities after keratoplasty. Recognition of these risk factors in advance of surgery will alert the surgeon to the need for appropriate management.