'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. We document a clear timeline of how we have worked together to co-create an animation and information sheet about receiving outpatient parenteral antimicrobial therapy (OPAT). We identify the opportunities and challenges we faced.

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 connectomes. The data that can comprise of up to 108 individual EM images must be assembled into a volume, requiring seamless 2D registration from physical section followed by 3D alignment of the stitched sections. The high throughput of ssEM necessitates 2D stitching to be done at the pace of imaging, which currently produces tens of terabytes per day. To achieve this, we present a modular volume assembly software pipeline ASAP (Assembly Stitching and Alignment Pipeline) that is scalable to datasets containing petabytes of data and parallelized to work in a distributed computational environment. The pipeline is built on top of the Render Trautman and Saalfeld (2019) services used in the volume assembly of the brain of adult Drosophila melanogaster (Zheng et al. 2018). It achieves high throughput by operating only on image meta-data and transformations. ASAP is modular, allowing for easy incorporation of new algorithms without significant changes in the workflow. The entire software pipeline includes a complete set of tools for stitching, automated quality control, 3D section alignment, and final rendering of the assembled volume to disk. ASAP has been deployed for continuous stitching of several large-scale datasets of the mouse visual cortex and human brain samples including one cubic millimeter of mouse visual cortex (Yin et al. 2020); Microns Consortium et al. (2021) at speeds that exceed imaging. The pipeline also has multi-channel processing capabilities and can be applied to fluorescence and multi-modal datasets like array tomography.

"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. Most of the "evidence" came from stories shared by parents and healthcare professionals. This paper draws on some elements of socio-narratology and is predicated on the basis that stories are important and they can act on and with us. By using an animation to tell Lily's story, the intention was to communicate research findings to a wider and more diverse audience than the typical readership of an academic journal. The intention was to act in and on people's consciousness about children's pain and to strengthen relationships and create bonds between clinicians, parents, and children in pain to make their dialog more social, connected, and meaningful. All three of us-the researcher, the writer, and the animator-have been marked and "re-shaped" by our work related to creating Lily; we have learned more about children like Lily and their mothers, and we have learned more about ourselves and our humanity. This animation is still a story in progress, a story 'in the wild', a story (and a resource) we would like you to re-tell and share. The story of Lily's pain aimed to change the lives of parents and children and professionals. Our hope is that you can be part of that change.

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. We conclude by reflecting on the kinds of spaces and skills that may be needed to work with this new understanding of failure and show that developing these is a crucial part of resisting neoliberalism and creating a more 'care-full' (Mountz et al., 2015) academy.

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. This effort has resulted in the identification of novel compounds and their hypothesized targets that will hopefully fuel future TB drug discovery and target validation programs alike.

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. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (http://developingmouse.brain-map.org).

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. Two additional drug-discovery-relevant datasets are included: a) a drug-like property analysis reflecting the latest lead-like guidelines and b) an early lead-generation package of the most promising hits within the clusters identified.

Antithrombotic potential of GW813893: a novel, orally active, active-site directed factor Xa inhibitor.

BACKGROUND: Factor Xa (FXa) has been a target of considerable interest for drug development efforts aimed at suppressing thrombosis. In this report, a new orally active, small molecule, active-site directed FXa inhibitor, GW813893, has been profiled in a succession of in vitro and in vivo assays involved in its preclinical characterization as a potential antithrombotic therapeutic. METHODS: In vitro profiling of GW813893 consisted of assessing its inhibitory potential against FXa and a broad panel of related and unrelated enzymes and receptors. Additionally, the FXa inhibition potential of GW813893 was assessed in prothrombinase and plasma-based clotting assays. In vivo characterization of GW813893 consisted of thrombosis studies in a rat inferior vena cava model, a rat carotid artery thrombosis model, and a rabbit jugular thrombosis model. Bleeding studies were conducted in a rat tail transection model. Ex vivo determinations of compound effects on FX and clotting activity were also undertaken. RESULTS: GW813893 was more than 90-fold selective over all enzymes tested, and it inhibited FXa and prothrombinase activity with a Ki of 4.0 nM and 9.7 nM, respectively. In vivo, GW813893 concentration-dependently suppressed thrombotic activity in all models tested. The antithrombotic activity correlated with the suppression of plasma-based clotting activity and the inhibition of plasma FX activity (P < 0.02). Over the antithrombotic dose-range, an increased bleeding diathesis was not observed. CONCLUSION: These experiments demonstrate that GW813893 is a potent, selective, orally active inhibitor of FXa. The data suggest that GW813893 has robust antithrombotic potential at doses that have no detectable hemostasis liability. Collectively, the profile suggests that GW813893 has the preclinical pharmacology underpinnings of an oral antithrombotic therapeutic.

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. In vivo optic disc imaging was performed by HRT2 and fundus camera photography. RESULTS: The optic nerve of the tree shrew comprised regions comparable to the human prelaminar and lamina cribrosa (LC) in the optic nerve head and the retrolaminar region, immediately posterior. The multilayered connective tissue plates of tree shrew LC stretched across the optic nerve canal at the level of the sclera and consisted of collagen types I, III, IV, V, and VI; elastin; and fibronectin. Significant age-related alterations in connective tissue components were indicated. Connective tissue was present in the central retinal vessel sheaths and was identified as longitudinally oriented collagen fibrils in the retrolaminar optic nerve. GFAP immunofluorescence indicated a high concentration of astrocytic processes in the LC. Myelination of axons was evident in the retrolaminar optic nerve. Ultrastructural studies supported the structural organization and spatial distribution of connective tissue. CONCLUSIONS: In contrast to many rodent models of glaucoma, since the tree shrew optic nerve resembles that in humans, especially at the LC, the tree shrew offers an ideal opportunity to investigate glaucoma pathophysiology in a subprimate model.