A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex.

To understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of activity in the awake mouse visual cortex: the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes the cortical activity of nearly 60,000 neurons from six visual areas, four layers, and 12 transgenic mouse lines in a total of 243 adult mice, in response to a systematic set of visual stimuli. We classify neurons on the basis of joint reliabilities to multiple stimuli and validate this functional classification with models of visual responses. While most classes are characterized by responses to specific subsets of the stimuli, the largest class is not reliably responsive to any of the stimuli and becomes progressively larger in higher visual areas. These classes reveal a functional organization wherein putative dorsal areas show specialization for visual motion signals.

Reforming a System That Cannot Reform Itself: Child Welfare Reform by Class Action Lawsuits.

Class action lawsuits have become an increasingly common way to facilitate institutional reform. The purpose of this article is to provide an introduction to social workers of child welfare reform by class action lawsuits and subsequent consent decrees. The authors provide an overview of class action lawsuits, with a focus on their role in implementing systematic change in the United States. They highlight consent decrees as a means of settling class action lawsuits. They illustrate the current state of the child welfare system and how child advocacy groups have used class action lawsuits to initiate reform. Authors provide two case examples of child welfare reform by consent decree and engage in comparative analysis to investigate similarities and differences in the two cases. Finally, they note implications for social work practice and education and provide recommendations to equip and train social workers involved in child welfare services.

Child Protective Service Referrals Involving Exposure to Domestic Violence: Prevalence, Associated Maltreatment Types, and Likelihood of Formal Case Openings.

Childhood exposure to domestic violence (CEDV) is widely understood as potentially harmful to children. Accordingly, many child welfare systems in the United States construe CEDV as maltreatment when the exposure results in harm or threatened harm to the child. The purpose of the current study was to investigate substantiated child welfare referrals directly related to CEDV to better understand the prevalence and patterns of CEDV-related maltreatment and how child welfare workers respond under the "harm or threatened harm" standard. Data were drawn from 23,704 substantiated referrals between 2009 and 2013 in a large Midwestern child welfare system. Approximately 20% of substantiated referrals were CEDV related. A plurality of CEDV-related referrals included both a male caregiver and female caregiver who were co-substantiated for maltreatment. The most common maltreatment types substantiated for these referrals were neglect based rather than abuse based, and just under a quarter (23%) of CEDV-related referrals were formally opened for services. Referrals involving co-occurring substance abuse were most likely to be opened for services based on predicted probabilities derived from multilevel modeling. Implications for policy and practice are considered.

The Allen Brain Atlas as a Resource for Teaching Undergraduate Neuroscience.

The open science movement has resulted in a growing field of data- and tool-sharing platforms that serve as a resource not only for sharing data and results in the field of brain science but has allowed students and researchers to learn neuroscientific skills and concepts. For over a decade, the Allen Institute for Brain Science has been meticulously collecting high quality data mapping gene expression, connectivity and, more recently, functional data from the brains of mice, macaques and humans. These open data have been paired with unique navigation and visualization tools such that the neuroscience researcher can explore, utilize and even incorporate these data into their publications. The tools created to explore and analyze the Allen Brain Atlas datasets have also been widely utilized to teach neuroscientific concepts to undergraduate and graduate students. This article aims to outline how to use the Allen Brain Atlas resources as teaching tools to impart neuroanatomic concepts to undergraduate and graduate neuroscience students.

Domestic violence, parental substance misuse and the decision to substantiate child maltreatment.

Families that experience domestic violence and parental substance misuse are disproportionately involved with the child welfare system. Prior research suggests that child protective services (CPS) caseworkers are more likely to substantiate maltreatment allegations when domestic violence and parental substance misuse are identified during the investigation, pointing to one possible mechanism for this disproportionate involvement. While previous studies have relied on nationally representative data sets, the current study used administrative records from a large Midwestern child welfare agency that accounts for state-level variation in child welfare policy and practice. A total of 501,060 substantiation decisions made between 2009 and 2013 were examined to assess the influence of caseworker-perceived domestic violence and parental substance misuse on the decision to substantiate reported maltreatment. Results from multilevel modeling suggest that the identification of domestic violence and parental substance misuse during an investigation significantly increased the probability that an allegation would be substantiated. The implication of these findings for child welfare practice are considered in light of the fact that many child welfare agencies do not consider exposure to domestic violence and parental substance misuse in and of themselves to constitute child maltreatment.

Neuropathological and transcriptomic characteristics of the aged brain.

As more people live longer, age-related neurodegenerative diseases are an increasingly important societal health issue. Treatments targeting specific pathologies such as amyloid beta in Alzheimer's disease (AD) have not led to effective treatments, and there is increasing evidence of a disconnect between traditional pathology and cognitive abilities with advancing age, indicative of individual variation in resilience to pathology. Here, we generated a comprehensive neuropathological, molecular, and transcriptomic characterization of hippocampus and two regions cortex in 107 aged donors (median = 90) from the Adult Changes in Thought (ACT) study as a freely-available resource (http://aging.brain-map.org/). We confirm established associations between AD pathology and dementia, albeit with increased, presumably aging-related variability, and identify sets of co-expressed genes correlated with pathological tau and inflammation markers. Finally, we demonstrate a relationship between dementia and RNA quality, and find common gene signatures, highlighting the importance of properly controlling for RNA quality when studying dementia.

Teaching with Big Data: Report from the 2016 Society for Neuroscience Teaching Workshop.

As part of a series of workshops on teaching neuroscience at the Society for Neuroscience annual meetings, William Grisham and Richard Olivo organized the 2016 workshop on "Teaching Neuroscience with Big Data." This article presents a summary of that workshop. Speakers provided overviews of open datasets that could be used in teaching undergraduate courses. These included resources that already appear in educational settings, including the Allen Brain Atlas (presented by Joshua Brumberg and Terri Gilbert), and the Mouse Brain Library and GeneNetwork (presented by Robert Williams). Other resources, such as NeuroData (presented by William R. Gray Roncal), and OpenFMRI, NeuroVault, and Neurosynth (presented by Russell Poldrack) have not been broadly utilized by the neuroscience education community but offer obvious potential. Finally, William Grisham discussed the iNeuro Project, an NSF-sponsored effort to develop the necessary curriculum for preparing students to handle Big Data. Linda Lanyon further elaborated on the current state and challenges in educating students to deal with Big Data and described some training resources provided by the International Neuroinformatics Coordinating Facility. Neuroinformatics is a subfield of neuroscience that deals with data utilizing analytical tools and computational models. The feasibility of offering neuroinformatics programs at primarily undergraduate institutions was also discussed.

A comprehensive transcriptional map of primate brain development.

The transcriptional underpinnings of brain development remain poorly understood, particularly in humans and closely related non-human primates. We describe a high-resolution transcriptional atlas of rhesus monkey (Macaca mulatta) brain development that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical division of cortical and subcortical regions associated with human neuropsychiatric disease. Gene expression changes more rapidly before birth, both in progenitor cells and maturing neurons. Cortical layers and areas acquire adult-like molecular profiles surprisingly late in postnatal development. Disparate cell populations exhibit distinct developmental timing of gene expression, but also unexpected synchrony of processes underlying neural circuit construction including cell projection and adhesion. Candidate risk genes for neurodevelopmental disorders including primary microcephaly, autism spectrum disorder, intellectual disability, and schizophrenia show disease-specific spatiotemporal enrichment within developing neocortex. Human developmental expression trajectories are more similar to monkey than rodent, although approximately 9% of genes show human-specific regulation with evidence for prolonged maturation or neoteny compared to monkey.

Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system.

The Allen Brain Atlas (http://www.brain-map.org) provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate. Here, we review the resources available at the Allen Brain Atlas, describing each product and data type [such as in situ hybridization (ISH) and supporting histology, microarray, RNA sequencing, reference atlases, projection mapping and magnetic resonance imaging]. In addition, standardized and unique features in the web applications are described that enable users to search and mine the various data sets. Features include both simple and sophisticated methods for gene searches, colorimetric and fluorescent ISH image viewers, graphical displays of ISH, microarray and RNA sequencing data, Brain Explorer software for 3D navigation of anatomy and gene expression, and an interactive reference atlas viewer. In addition, cross data set searches enable users to query multiple Allen Brain Atlas data sets simultaneously. All of the Allen Brain Atlas resources can be accessed through the Allen Brain Atlas data portal.

The human brain online: an open resource for advancing brain research.

This community page describes the database and associated Web application that comprise the Allen Human Brain Atlas, an open online resource that integrates genomic and anatomic human brain data.