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Velká potřebnost koordinace standardů a osvědčených postupů v neurovědách souvisí s úsilím o to, aby se neurovědy staly disciplínou zaměřenou na data. Globální iniciativy a projekty ve výzkumu mozku jsou připraveny generovat obrovské množství neurovědeckých dat. Zároveň se neurovědy, stejně jako mnohé domény v biomedicíně, potýkají s otázkami transparentnosti, přesnosti a reprodukovatelnosti. Široce používané a validované standardy a osvědčené postupy jsou klíčem k řešení výzev ve výzkumu, který využívá velká i malá data, protože tyto standardy a postupy jsou nezbytné pro integraci různých dat a pro rozvoj robustní, efektivní a udržitelné infrastruktury podporující otevřené a reprodukovatelné neurovědy. Vypracování komunitních standardů a jejich přijetí je však obtížné. Současná situace se vyznačuje nedostatkem robustních, validovaných standardů a množstvím překrývajících se, nedostatečně rozvinutých, nevyzkoušených a nedostatečně využívaných standardů a osvědčených postupů. International Neuroinformatics Coordinating Facility (INCF), nezávislá organizace zaměřená na podporu sdílení dat prostřednictvím koordinace infrastruktury a standardů, nedávno zavedla formální proces pro hodnocení a schvalování komunitních standardů a osvědčených postupů podporující FAIR principy. Tím, že INCF formálně slouží jako standardizační organizace zaměřená na otevřené a FAIR neurovědy, pomáhá hodnotit, propagovat a koordinovat standardy a osvědčené postupy napříč neurovědami. Tento článek poskytuje přehled o tomto procesu a diskutuje o tom, jak můžou neurovědy těžit z existence specializované standardizačního orgánu. There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the issues of transparency, rigor, and reproducibility. Widely used, validated standards and best practices are key to addressing the challenges in both big and small data science, as they are essential for integrating diverse data and for developing a robust, effective, and sustainable infrastructure to support open and reproducible neuroscience. However, developing community standards and gaining their adoption is difficult. The current landscape is characterized both by a lack of robust, validated standards and a plethora of overlapping, underdeveloped, untested and underutilized standards and best practices. The International Neuroinformatics Coordinating Facility (INCF), an independent organization dedicated to promoting data sharing through the coordination of infrastructure and standards, has recently implemented a formal procedure for evaluating and endorsing community standards and best practices in support of the FAIR principles. By formally serving as a standards organization dedicated to open and FAIR neuroscience, INCF helps evaluate, promulgate, and coordinate standards and best practices across neuroscience. Here, we provide an overview of the process and discuss how neuroscience can benefit from having a dedicated standards body.

There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the issues of transparency, rigor, and reproducibility. Widely used, validated standards and best practices are key to addressing the challenges in both big and small data science, as they are essential for integrating diverse data and for developing a robust, effective, and sustainable infrastructure to support open and reproducible neuroscience. However, developing community standards and gaining their adoption is difficult. The current landscape is characterized both by a lack of robust, validated standards and a plethora of overlapping, underdeveloped, untested and underutilized standards and best practices. The International Neuroinformatics Coordinating Facility (INCF), an independent organization dedicated to promoting data sharing through the coordination of infrastructure and standards, has recently implemented a formal procedure for evaluating and endorsing community standards and best practices in support of the FAIR principles. By formally serving as a standards organization dedicated to open and FAIR neuroscience, INCF helps evaluate, promulgate, and coordinate standards and best practices across neuroscience. Here, we provide an overview of the process and discuss how neuroscience can benefit from having a dedicated standards body.

Objectives: A vendor informed us that rats shipped to us and used by us in a spinal cord contusion injury experiment were infected by rat parvovirus type 1a (RPV-1a). Our aim was therefore to determine whether this infection may have altered locomotor recovery or tissue pathology. Setting: Stockholm, Sweden. Methods: We induced a moderate contusion injury of the spinal cord in rats received from an (unknown to us) RPV-1a-contaminated facility. We compared the hind limb locomotor function between RPV-1a-infected rats and non-infected controls with the same spinal cord lesions, obtained before (historical control), as well as after infection (future controls). Histologically, we assessed spinal tissue sparing, astrocyte reactivity and the amount of macrophages/activated microglia. Results: RPV-1a-infected rats had significantly better hind limb locomotor recovery compared with both ‘historical' and ‘future' controls. We also observed significantly better tissue sparing and axonal sparing around the injury site, as well as significant reductions in macrophages/activated microglia and astrocyte reactivity in the spinal cords of RPV-1a-infected rats. Conclusion: The results stress the importance of knowing the health status of animals used to study central nervous system trauma and support the notion that acquired infections, even if asymptomatic, may alter response to injury in mammals. Furthermore, the results demonstrate that virus infections may have positive effects on functional recovery after spinal cord injury and indicate that RPV-1a infection may be neuroprotective by dampening secondary damage.

With no currently available drug treatment for spinal cord injury, there is a need for additional therapeutic candidates. We took the approach of repositioning existing pharmacological agents to serve as acute treatments for spinal cord injury and previously found imatinib to have positive effects on locomotor and bladder function in experimental spinal cord injury when administered immediately after the injury. However, for imatinib to have translational value, it needs to have sustained beneficial effects with delayed initiation of treatment, as well. Here, we show that imatinib improves hind limb locomotion and bladder recovery when initiation of treatment was delayed until 4 h after injury and that bladder function was improved with a delay of up to 24 h. The treatment did not induce hypersensitivity. Instead, imatinib-treated animals were generally less hypersensitive to either thermal or mechanical stimuli, compared with controls. In an effort to provide potential biomarkers, we found serum levels of three cytokines/chemokines—monocyte chemoattractant protein-1, macrophage inflammatory protein (MIP)-3α, and keratinocyte chemoattractant/growth-regulated oncogene (interleukin 8)—to increase over time with imatinib treatment and to be significantly higher in injured imatinib-treated animals than in controls during the early treatment period. This correlated to macrophage activation and autofluorescence in lymphoid organs. At the site of injury in the spinal cord, macrophage activation was instead reduced by imatinib treatment. Our data strengthen the case for clinical trials of imatinib by showing that initiation of treatment can be delayed and by identifying serum cytokines that may serve as candidate markers of effective imatinib doses.

Article history: Received 31 March 2014 Revised 24 April 2014 Accepted 25 April 2014 Available online 11 May 2014 studies (Benowitz, 2012; Bunge and Pearse, 2012; Erschbamer et al., 2012), pointing out weaknesses in the re-assessment studies including incomplete replication of the basis of the original experiments, too much variability, too little power and other suboptimal circumstances. In the following, we wish to comment on the reassessment (Sharp et al., 2014a) of our imatinib study (Abrams et al., 2012). We assisted the re-assessment team by responding to questions about details

A number of different rodent experimental models of spinal cord injury have been used in an attempt to model the pathophysiology of human spinal cord injury. As a result, interlaboratory comparisons of the outcome measures can be difficult. Further complicating interexperiment comparisons is the fact that the rodent response to different experimental models is strain-dependent. Moreover, the literature is abundant with examples in which the same injury model and strain result in divergent functional outcomes. The objective of this research was to determine whether substrain differences influence functional outcome in experimental spinal cord injury. We induced mild contusion spinal cord injuries in three substrains of Sprague-Dawley rats purchased from three different European breeders (Scanbur, Charles River, and Harlan) and evaluated the impact of injury on spontaneous locomotor function, hypersensitivity to mechanical stimulation, and bladder function. We found that Harlan rats regained significantly more hindlimb function than Charles River and Scanbur rats. We also observed substrain differences in the recovery of the ability to empty the bladder and development of hypersensitivity to mechanical stimulation. The Harlan substrain did not show any signs of hypersensitivity in contrast to the Scanbur and Charles River substrains, which both showed transient reduction in paw withdrawal thresholds. Lastly, we found histological differences possibly explaining the observed behavioral differences. We conclude that in spite of being the same strain, there might be genetic differences that can influence outcome measures in experimental studies of spinal cord injury of Sprague-Dawley rats from different vendors.

Many areas of neuroscience are now critically dependent on computational tools to help understand the large volumes of data being created. Furthermore, computer models are increasingly being used to help predict and understand the function of the nervous system. Many of these computations are complex and often cannot be concisely reported in the methods section of a scientific article. In a few areas there are widely used software packages for analysis (e.g., SPM, FSL, AFNI, BrainVoyager, FreeSurfer in neuroimaging) or simulation (e.g. NEURON, NEST, Brian). However, we often write new computer programs to solve specific problems in the course of our research. Some of these programs may be relatively small scripts that help analyze all of our data, and these rarely get described in papers. As authors, how best can we maximize the chances that other scientists can reproduce our computations or reuse our methods on their data? Is our research reproducible? Our article lists practical suggestions to maximise the reproducibility of our work.