Quantifying brain development in the HEALthy Brain and Child Development (HBCD) Study: The magnetic resonance imaging and spectroscopy protocol.

The HEALthy Brain and Child Development (HBCD) Study, a multi-site prospective longitudinal cohort study, will examine human brain, cognitive, behavioral, social, and emotional development beginning prenatally and planned through early childhood. The acquisition of multimodal magnetic resonance-based brain development data is central to the study's core protocol. However, application of Magnetic Resonance Imaging (MRI) methods in this population is complicated by technical challenges and difficulties of imaging in early life.

Web-based processing of physiological noise in fMRI: addition of the PhysIO toolbox to CBRAIN.

Neuroimaging research requires sophisticated tools for analyzing complex data, but efficiently leveraging these tools can be a major challenge, especially on large datasets. CBRAIN is a web-based platform designed to simplify the use and accessibility of neuroimaging research tools for large-scale, collaborative studies. In this paper, we describe how CBRAIN's unique features and infrastructure were leveraged to integrate TAPAS PhysIO, an open-source MATLAB toolbox for physiological noise modeling in fMRI data.

Mitochondrial genome annotation with MFannot: a critical analysis of gene identification and gene model prediction.

Compared to nuclear genomes, mitochondrial genomes (mitogenomes) are small and usually code for only a few dozen genes. Still, identifying genes and their structure can be challenging and time-consuming. Even automated tools for mitochondrial genome annotation often require manual analysis and curation by skilled experts.

Differential associations of adolescent versus young adult cannabis initiation with longitudinal brain change and behavior.

Leveraging ~10 years of prospective longitudinal data on 704 participants, we examined the effects of adolescent versus young adult cannabis initiation on MRI-assessed cortical thickness development and behavior. Data were obtained from the IMAGEN study conducted across eight European sites. We identified IMAGEN participants who reported being cannabis-naïve at baseline and had data available at baseline, 5-year, and 9-year follow-up visits.

Data and Tools Integration in the Canadian Open Neuroscience Platform.

We present the Canadian Open Neuroscience Platform (CONP) portal to answer the research community's need for flexible data sharing resources and provide advanced tools for search and processing infrastructure capacity. This portal differs from previous data sharing projects as it integrates datasets originating from a number of already existing platforms or databases through DataLad, a file level data integrity and access layer. The portal is also an entry point for searching and accessing a large number of standardized and containerized software and links to a computing infrastructure.

Conduct problems are associated with accelerated thinning of emotion-related cortical regions in a community-based sample of adolescents.

Few studies have examined the association between conduct problems and cerebral cortical development. Herein, we characterize the association between age-related brain change and conduct problems in a large longitudinal, community-based sample of adolescents. 1,039 participants from the IMAGEN study possessed psychopathology and surface-based morphometric data at study baseline (M = 14.

Refining Mitochondrial Intron Classification With ERPIN: Identification Based on Conservation of Sequence Plus Secondary Structure Motifs.

Mitochondrial genomes-in particular those of fungi-often encode genes with a large number of Group I and Group II introns that are conserved at both the sequence and the RNA structure level. They provide a rich resource for the investigation of intron and gene structure, self- and protein-guided splicing mechanisms, and intron evolution. Yet, the degree of sequence conservation of introns is limited, and the primary sequence differs considerably among the distinct intron sub-groups.

A Simulation Toolkit for Testing the Sensitivity and Accuracy of Corticometry Pipelines.

In recent years, the replicability of neuroimaging findings has become an important concern to the research community. Neuroimaging pipelines consist of myriad numerical procedures, which can have a cumulative effect on the accuracy of findings. To address this problem, we propose a method for simulating artificial lesions in the brain in order to estimate the sensitivity and specificity of lesion detection, using different automated corticometry pipelines.

Association of Cannabis Use During Adolescence With Neurodevelopment.

Importance: Animal studies have shown that the adolescent brain is sensitive to disruptions in endocannabinoid signaling, resulting in altered neurodevelopment and lasting behavioral effects. However, few studies have investigated ties between cannabis use and adolescent brain development in humans.

Objective: To examine the degree to which magnetic resonance (MR) imaging-assessed cerebral cortical thickness development is associated with cannabis use in a longitudinal sample of adolescents.

Comparing perturbation models for evaluating stability of neuroimaging pipelines.

With an increase in awareness regarding a troubling lack of reproducibility in analytical software tools, the degree of validity in scientific derivatives and their downstream results has become unclear. The nature of reproducibility issues may vary across domains, tools, data sets, and computational infrastructures, but numerical instabilities are thought to be a core contributor. In neuroimaging, unexpected deviations have been observed when varying operating systems, software implementations, or adding negligible quantities of noise.

Amygdalar reactivity is associated with prefrontal cortical thickness in a large population-based sample of adolescents.

In structural neuroimaging studies, reduced cerebral cortical thickness in orbital and ventromedial prefrontal regions is frequently interpreted as reflecting an impaired ability to downregulate neuronal activity in the amygdalae. Unfortunately, little research has been conducted in order to test this conjecture. We examine the extent to which amygdalar reactivity is associated with cortical thickness in a population-based sample of adolescents.

White matter microstructure is associated with hyperactive/inattentive symptomatology and polygenic risk for attention-deficit/hyperactivity disorder in a population-based sample of adolescents.

Few studies have investigated the link between putative biomarkers of attention-deficit/hyperactivity disorder (ADHD) symptomatology and genetic risk for ADHD. To address this, we investigate the degree to which ADHD symptomatology is associated with white matter microstructure and cerebral cortical thickness in a large population-based sample of adolescents. Critically, we then test the extent to which multimodal correlates of ADHD symptomatology are related to ADHD polygenic risk score (PRS).

Integration of Data and Phenotypic Data Within a Unified Extensible Multimodal Framework.

Analysis of "" data is often a long and segmented process, encompassing multiple stages from initial data collection to processing, quality control and visualization. The cross-modal nature of recent genomic analyses renders this process challenging to both automate and standardize; consequently, users often resort to manual interventions that compromise data reliability and reproducibility. This in turn can produce multiple versions of datasets across storage systems.

Boutiques: a flexible framework to integrate command-line applications in computing platforms.

We present Boutiques, a system to automatically publish, integrate, and execute command-line applications across computational platforms. Boutiques applications are installed through software containers described in a rich and flexible JSON language. A set of core tools facilitates the construction, validation, import, execution, and publishing of applications.

Cyberinfrastructure for Open Science at the Montreal Neurological Institute.

Data sharing is becoming more of a requirement as technologies mature and as global research and communications diversify. As a result, researchers are looking for practical solutions, not only to enhance scientific collaborations, but also to acquire larger amounts of data, and to access specialized datasets. In many cases, the realities of data acquisition present a significant burden, therefore gaining access to public datasets allows for more robust analyses and broadly enriched data exploration.

The MNI data-sharing and processing ecosystem.

Neuroimaging has been facing a data deluge characterized by the exponential growth of both raw and processed data. As a result, mining the massive quantities of digital data collected in these studies offers unprecedented opportunities and has become paramount for today's research. As the neuroimaging community enters the world of "Big Data", there has been a concerted push for enhanced sharing initiatives, whether within a multisite study, across studies, or federated and shared publicly.

Reproducibility of neuroimaging analyses across operating systems.

Neuroimaging pipelines are known to generate different results depending on the computing platform where they are compiled and executed. We quantify these differences for brain tissue classification, fMRI analysis, and cortical thickness (CT) extraction, using three of the main neuroimaging packages (FSL, Freesurfer and CIVET) and different versions of GNU/Linux. We also identify some causes of these differences using library and system call interception.

CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research.

The Canadian Brain Imaging Research Platform (CBRAIN) is a web-based collaborative research platform developed in response to the challenges raised by data-heavy, compute-intensive neuroimaging research. CBRAIN offers transparent access to remote data sources, distributed computing sites, and an array of processing and visualization tools within a controlled, secure environment. Its web interface is accessible through any modern browser and uses graphical interface idioms to reduce the technical expertise required to perform large-scale computational analyses.

Heritable changes in regional cortical thickness with age.

It is now well established that regional indices of brain structure such as cortical thickness, surface area or grey matter volume exhibit spatially variable patterns of heritability. However, a recent study found these patterns to change with age during development, a result supported by gene expression studies. Changes in heritability have not been investigated in adulthood so far and could have important implications in the study of heritability and genetic correlations in the brain as well as in the discovery of specific genes explaining them.

In situ quantification of mitochondrial respiration in permeabilized fibers of a marine invertebrate with low aerobic capacity.

The aim of this study was to design a protocol to allow the assessment of normal and alternative pathways for electron transport in mitochondria using an in situ approach (on permeabilized fibers) in high-resolution respirometry. We measured the oxygen consumption of permeabilized fibers from Nereis (Neanthes) virens with different substrates and the presence of ADP. To estimate the alternative oxidase (AOX) activity, antimycin A was introduced in order to inhibit complex III.

Not only students can express alcohol dehydrogenase: goldfish can too!

This article describes a novel approach to study the metabolic regulation of the respiratory system in vertebrates that suits physiology lessons for undergraduate students. It consists of an experimental demonstration of the goldfish's (Carassius auratus) adaptations to anoxia. The goldfish is one of the few vertebrates showing strong enzymatic plasticity for the expression of alcohol dehydrogenase (ADH), which allows it to survive long periods of severe anoxia.

Multifaceted inpatient psychiatry approach to reducing readmissions: a pilot study.

Context: Access to psychiatric services, particularly inpatient psychiatric care, is limited and lacks comprehensiveness in rural areas.

Purpose: The purpose of this study was to evaluate the impact on readmission rates of a multifaceted inpatient psychiatry approach (MIPA) offered in a rural hospital.

Methods: Readmissions within 30 days of patients who were admitted to an inpatient psychiatric unit using a MIPA model of care (N = 147) were compared to readmissions of a comparison group of patients who were admitted prior to the adoption of the MIPA (N = 37).

Energetic metabolism and biochemical adaptation: A bird flight muscle model.

The main objective of this class experiment is to measure the activity of two metabolic enzymes in crude extract from bird pectoral muscle and to relate the differences to their mode of locomotion and ecology. The laboratory is adapted to stimulate the interest of wildlife management students to biochemistry. The enzymatic activities of cytochrome c oxidase and lactate dehydrogenase are measured in pectoral muscle of black duck and ring-necked pheasant.

An atypical form of erythrokeratodermia variabilis maps to chromosome 7q22.

Erythrokeratodermia variabilis 3 (Kamouraska type) or EKV3 is a newly described autosomal recessive disorder observed in patients from the Bas St-Laurent region of Quebec. It has similar skin lesions as observed for EKV, including congenital hyperkeratosis and red patches of variable sizes, shapes, and duration. EKV3 is also characterized by ichthyosis, sensorineural hearing loss, peripheral neuropathy, psychomotor retardation, congenital chronic diarrhea, and an elevation of very long chain fatty acids (VLCFAs).

Progesterone in milk: a simple experiment illustrating the estrous cycle and enzyme immunoassay.

Experiments designed for students in reproductive physiology are rare. Here, we describe a simple experiment concerning a physiological aspect of the reproductive system. Milk samples are obtained from cows in estrus, in midcycle, 21 days after insemination, and in gestation.