A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain.

The mammalian brain consists of millions to billions of cells that are organized into many cell types with specific spatial distribution patterns and structural and functional properties. Here we report a comprehensive and high-resolution transcriptomic and spatial cell-type atlas for the whole adult mouse brain. The cell-type atlas was created by combining a single-cell RNA-sequencing (scRNA-seq) dataset of around 7 million cells profiled (approximately 4.

'ZOOMing' in on Consulting with Children and Parents Remotely to Co-Create Health Information Resources.

The COVID-19 pandemic altered the way many people worked. Remote and creative ways were favoured and utilised for consultation activities. In this paper, we draw attention to how we have used creative methods over the teleconferencing platform 'ZOOM' to consult with children and their parents when we were unable to consult with them face-to-face.

A scalable and modular automated pipeline for stitching of large electron microscopy datasets.

Serial-section electron microscopy (ssEM) is the method of choice for studying macroscopic biological samples at extremely high resolution in three dimensions. In the nervous system, nanometer-scale images are necessary to reconstruct dense neural wiring diagrams in the brain, so -called . The data that can comprise of up to 10 individual EM images must be assembled into a volume, requiring seamless 2D registration from physical section followed by 3D alignment of the stitched sections.

"Communicating Lily's Pain": A reflective narrative commentary about co-creating a resource to provoke thinking and change about assessing and managing the pain of children with profound cognitive impairment.

This paper draws together about 20 years of research work and discovery and the development of a resource about pain assessment and management in children with profound cognitive impairment. The animation tells the story of an imagined child called Lily and the skills her mother uses and the challenges that her mother faces in assessing and managing Lily's pain. The animation is built on stories drawn from qualitative research findings, conversations while in clinical practice and with members of the general public, parent advisers and other sources.

Survey of spiking in the mouse visual system reveals functional hierarchy.

The anatomy of the mammalian visual system, from the retina to the neocortex, is organized hierarchically. However, direct observation of cellular-level functional interactions across this hierarchy is lacking due to the challenge of simultaneously recording activity across numerous regions. Here we describe a large, open dataset-part of the Allen Brain Observatory-that surveys spiking from tens of thousands of units in six cortical and two thalamic regions in the brains of mice responding to a battery of visual stimuli.

The 'present-tense' experience of failure in the university: Reflections from an action research project.

This article reflects on insights from an action research project where we worked with students whose university experience was inhibited by the fear of failure. In contrast to the popular concept of 'learning from failure', which involves intellectualizing the experience and distancing ourselves from it, our findings demonstrate the importance of a 'present tense' focus on emotions and affects in order to understand the experience of failure for students. Doing so brings us face-to-face with the often painful experience of failure in the present moment which, we argue, is an important and valid part of the university experience.

Classification of electrophysiological and morphological neuron types in the mouse visual cortex.

Understanding the diversity of cell types in the brain has been an enduring challenge and requires detailed characterization of individual neurons in multiple dimensions. To systematically profile morpho-electric properties of mammalian neurons, we established a single-cell characterization pipeline using standardized patch-clamp recordings in brain slices and biocytin-based neuronal reconstructions. We built a publicly accessible online database, the Allen Cell Types Database, to display these datasets.

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.

Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery.

As a follow up to the antimycobacterial screening exercise and the release of GSK´s first Tres Cantos Antimycobacterial Set (TCAMS-TB), this paper presents the results of a second antitubercular screening effort of two hundred and fifty thousand compounds recently added to the GSK collection. The compounds were further prioritized based on not only antitubercular potency but also on physicochemical characteristics. The 50 most attractive compounds were then progressed for evaluation in three different predictive computational biology algorithms based on structural similarity or GSK historical biological assay data in order to determine their possible mechanisms of action.

Neurodata Without Borders: Creating a Common Data Format for Neurophysiology.

The Neurodata Without Borders (NWB) initiative promotes data standardization in neuroscience to increase research reproducibility and opportunities. In the first NWB pilot project, neurophysiologists and software developers produced a common data format for recordings and metadata of cellular electrophysiology and optical imaging experiments. The format specification, application programming interfaces, and sample datasets have been released.

A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain.

To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for ∼2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified.

Fueling open-source drug discovery: 177 small-molecule leads against tuberculosis.

With the aim of fuelling open-source, translational, early-stage drug discovery activities, the results of the recently completed antimycobacterial phenotypic screening campaign against Mycobacterium bovis BCG with hit confirmation in M. tuberculosis H37Rv were made publicly accessible. A set of 177 potent non-cytotoxic H37Rv hits was identified and will be made available to maximize the potential impact of the compounds toward a chemical genetics/proteomics exercise, while at the same time providing a plethora of potential starting points for new synthetic lead-generation activities.

Connective tissue structure of the tree shrew optic nerve and associated ageing changes.

Purpose: To identify the structure and composition of the tree shrew optic nerve to determine its potential as a model for glaucoma.

Methods: Tree shrew optic nerves, aged 4 weeks to 5 years, were wax or cryoembedded for analysis of overall morphology and cellular (glial fibrillary acidic protein [GFAP]) and extracellular matrix (collagen types I, III, IV, V, VI; fibronectin; and elastin) immunolocalization studies. In addition, transmission and scanning electron microscopy were performed.

Genome-wide atlas of gene expression in the adult mouse brain.

Molecular approaches to understanding the functional circuitry of the nervous system promise new insights into the relationship between genes, brain and behaviour. The cellular diversity of the brain necessitates a cellular resolution approach towards understanding the functional genomics of the nervous system. We describe here an anatomically comprehensive digital atlas containing the expression patterns of approximately 20,000 genes in the adult mouse brain.