Minimum information about a spinal cord injury experiment: a proposed reporting standard for spinal cord injury experiments.

Journal of Neurotrauma Minimum Information About a Spinal Cord Injury Experiment (MIASCI) – a proposed reporting standard for spinal cord injury experiments (doi: 10.1089/neu.2014.3400) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof.

Page 1 of 17

1 Minimum Information About a Spinal Cord Injury Experiment (MIASCI) – a proposed reporting standard for spinal cord injury experiments Vance P. Lemmon1*, Adam R. Ferguson2, Phillip G. Popovich3, Xiao-Ming Xu4, Diane M. Snow5, Michihiro Igarashi6, Christine E. Beattie7, John L. Bixby1* 1

Miami Project to Cure Paralysis, University of Miami School of Medicine, Miami, FL, 33136, USA, 2 Brain and Spinal Injury Center (BASIC), Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94110, USA, 3 Center for Brain and Spinal Cord Repair and the Department of Neuroscience, The Ohio State University, Columbus, OH, 43210, USA, 4 Stark Neurosciences Research Institute, Indiana University, Indianapolis, IN, 46202, USA 5 Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40636, USA, 6 Molecular and Cellular Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, 51-8510, Japan 7 Department of Neuroscience, The Ohio State University, Columbus, OH, 43210, USA, *co-corresponding authors MIASCI Consortium Saminda W. Abeyruwan, Computer Sciences, University of Miami, Coral Gables, FL USA Michael S. Beattie, Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA John R. Bethea, Biology, Drexel University, Philadelphia, PA, USA Frank Bradke, Axon Growth and Regeneration, German Center for Neurodegenerative Diseases, Bonn, Germany Jacqueline C. Bresnahan, Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA Mary B. Bunge, Miami Project to Cure Paralysis, University of Miami, Miami, FL USA Alison Callahan, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA Samuel David, Centre for Research in Neuroscience, McGill University, Montreal, Quebec, Canada Sarah A. Dunlop, Experimental & Regenerative, Neurosciences, University of Western Australia, Crawley, WA, Australia James W. Fawcett, Centre for Brain Repair, Cambridge University, Cambridge, United Kingdom Michael G. Fehlings, Neurosurgery, University of Toronto, Toronto, Ontario, Canada Itzhak Fischer, Neurobiology and Anatomy, Drexel University, College of Medicine, Philadelphia, PA USA Paul Forscher, Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA, 06511 1


Page 2 of 17

2 Roman J. Giger, Cell and Developmental Biology University of Michigan Ann Arbor MI USA Yoshio Goshima, Molecular Pharmacology & Neurobiology, Yokohama City University Graduate School of Medicine, Yokohama, Japan Barbara Grimpe, Applied Neurobiology, University Medical Center Düsseldorf, Düsseldorf, Germany Theo Hagg, Department of Biomedical Sciences, East Tennessee State University, Johnson City, TN USA Edward D. Hall Anatomy & Neurobiology, Neurosurgery, Neurology and Physical Medicine & Rehabilitation, University of Kentucky, Lexington, KY, USA Benjamin J. Harrison, Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY USA Alan R. Harvey, Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, WA, Australia Cheng He, Neurobiology Second Military Medical University, Shanghai, China Zhigang He, F. M. Kirby Neurobiology Center, Boston Children¹s Hospital, Harvard Medical School, Boston, MA USA Tatsumi Hirata, Division of Brain Function, National Institute of Genetics, Mishima, Shizuoka, Japan Ahmet Hoke, Neurology and Neuroscience, Johns Hopkins University, Baltimore, MD USA Claire E. Hulsebosch, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas USA Andres Hurtado, Neurology Johns Hopkins University, Baltimore, MD USA Anjana Jain, Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA USA Ken Kadoya, Neurosciences, University of California, San Diego, San Diego, CA USA Hiroyuki Kamiguchi, Laboratory for Neuronal Growth Mechanisms RIKEN Brain Science Institute, Wako, Saitama, Japan Mineko Kengaku, Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan Jeffery D. Kocsis, Neurology, Yale University, West Haven, CT, USA Brian K. Kwon, Orthopedics, University of British, Columbia, Vancouver, BC Canada Jae Lee, Miami Project to Cure Paralysis, Neurological Surgery, University of Miami, Miami, FL USA Daniel J. Liebl, Miami Project to Cure Paralysis, Neurological Surgery, University of Miami, Miami, FL USA Shao-Jun Liu, Department of Neurobiology, The Academy of Military Medical Sciences, Beijing, China Laura A. Lowery, Biology, Boston College, Chestnut Hill, MA USA Shweta Mandrekar-Colucci, Center for Brain and Spinal Cord Repair, Department of Neuroscience, Ohio State University, Columbus, OH USA John H. Martin Physiology, Pharmacology & Neuroscience, The City College of the City University of New York, New York, NY USA Carol A. Mason, Pathology and Cell Biology, Neuroscience, and Ophthalmic Science Columbia University, New York, NY USA Dana M. McTigue, Neuroscience, Ohio State University, Columbus, OH USA Nassir Mokarram, The Wallace H. Coulter, Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA USA Lawrence D. Moon, Wolfson Centre for Age-Related Diseases, King's College London, University of London, London, United Kingdom Hans W. Muller, Neurology, Heinrich-Heine-University, Düsseldorf, Germany 2


Page 3 of 17

3 Takeshi Nakamura, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, USA Takashi Namba, Cell Pharmacology, Nagoya University, Nagoya, Japan Mariko Nishibe, Molecular Neuroscience, Osaka University, Osaka, Japan Izumi Oinuma, Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan Martin Oudega, Physical Medicine and Rehabilitation, Neurobiology, and Bioengineering, University of Pittsburgh, Pittsburgh, PA USA David E. Pleasure, Neurology and Pediatrics, University of California, Davis, Sacramento, CA USA Geoffrey Raisman Spinal Repair Unit, Institute of Neurology, University College London, London, United Kingdom Matthew N. Rasband, Neuroscience, Developmental Biology, and Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA Paul J. Reier, Neuroscience, University of Florida, Gainesville, FL USA Miguel Santiago-Medina, Neuroscience, University of Wisconsin, Madison, WI USA Jan M. Schwab, Department of Neurology with Experimental Neurology, Charité Universitätsmedizin Berlin, Berlin, Germany Martin E. Schwab, Brain Research Institute, University of Zurich, Zurich, Switzerland Yohei Shinmyo, Developmental Neurobiology, Kumamoto University, Kumamoto, Japan Jerry Silver, Neurosciences, Case Western Reserve University, Cleveland OH USA George M. Smith, Neuroscience, Temple University, Philadelphia, PA USA Kwok-Fai So, GHM Institute of CNS Regeneration, Jinan University, Guangzhou, Guangdong, China Michael V. Sofroniew, Neurobiology, University of California, Los Angeles, Los Angeles, CA USA Stephen M. Strittmatter, Cellular Neuroscience, Neurodegeneration and Repair, Yale University, New Haven, CT USA Mark H. Tuszynski, Center for Neural Repair, Neurosciences, University of California, San Diego, San Diego, CA USA Jeffery L. Twiss, Biological Sciences, University of South Carolina, Columbus, SC USA Ubbo Visser, Computer Science, University of Miami, Miami, FL USA Trent A. Watkins, Neuroscience, Genentech, Inc. South San Francisco, CA USA Wutian Wu, Anatomy, The University of Hong Kong, Hong Kong, China Sung Ok Yoon, Molecular & Cellular Biochemistry, Ohio State University, Columbus, OH USA Michisuke Yuzaki, Neurophysiology, Keio University, Tokyo, Japan Binhai Zheng, Neurosciences, University of California, San Diego San Diego CA USA Fengquan Zhou, Orthopedic Surgery & Neuroscience, Johns Hopkins University, Baltimore, MD USA Yimin Zou, Neurobiology Section, Division of Biological Sciences, University of California, San Diego, San Diego CA USA

3


Page 4 of 17

4 Abstract The lack of reproducibility in many areas of experimental science has a number of causes, including a lack of transparency and precision in the description of experimental approaches. This has farreaching consequences, including wasted resources and slowing of progress. Additionally, the large number of laboratories around the world publishing papers on a given topic make it difficult, if not impossible, for individual researchers to read all of the relevant literature. Consequently, centralized databases are needed to facilitate the generation of new hypotheses for testing. One strategy to improve transparency in experimental description, and to allow the development of frameworks for computer-readable knowledge repositories, is the adoption of uniform reporting standards, such as common data elements (data elements used in multiple clinical studies) and minimum information standards. This paper describes a minimum information standard for spinal cord injury (SCI) experiments, its major elements and the approaches used to develop it. Transparent reporting standards for experiments using animal models of human SCI aim to reduce inherent bias and increase experimental value. Introduction: The lack of reproducibility in science has been recognized for decades 1-3. Recently, this issue has been highlighted by scientists in pharmaceutical companies who reported that the majority of published basic biomedical science experiments identifying potential therapeutic targets could not be replicated 4, 5. Similarly, a project funded by the National Institute of Neurological Disorders and Stroke (NINDS) resulted in a high failure rate in replicating published preclinical results for treatment of spinal cord injury (SCI) 6. Strikingly, studies using RhoA/Rock inhibitors or stem cells to treat SCI have more favorable outcomes if the papers do not report whether investigators are blinded during behavioral testing 7, 8. Challenges in interpreting primary endpoints of morphological and functional neurological regeneration make careful documentation of methods used in SCI experiments essential 9-11. In addition, concerns have been raised about a number of issues in neuroscience publications including inappropriate statistics 12, 13, low power (calculated from 49 meta-analyses of 739 primary studies to be 21% 14) and a call to decrease p values from the commonly used 0.05 to 0.005-0.001 15. Changes in standard practices are needed to improve reproducibility and thus the translation of basic SCI research to the clinic16. Leaders in the neuroscience community have recommended specific changes in the way basic science studies are conducted and reported 6, 17, 18. In the larger scientific community there has been extensive discussion of strategies to improve reproducibility. For example, litter-to-litter variability can have a large impact on animal behavioral studies 19. Remarkably, between 2008 and 2013 there were at least 20 peer-reviewed publications presenting guidelines for in vivo preclinical studies20. Common recommendations included appropriate sample size, randomization of animals to groups, the use of positive and negative controls, and blinding of scientists to treatments during outcome assessments. In addition, the general lack of data availability is a major hindrance to interpretation and reanalysis of published experiments. Critical metadata regarding how experiments are done are often missing from published methods, and the raw data underlying graphs and figures are rarely included in publications. Many journals stipulate that primary data associated with a publication, such as microarray data, must be posted in public databases. However, an analysis of publications in the 50 4


Page 5 of 17

5 journals with the highest impact factors in 2009 revealed poor compliance (only 47/500 papers) with full deposition of primary data21. Scientists and clinicians conducting clinical trials have had to comply with standardized design and reporting guidelines for many years. For example, a common data element (CDE) system is in place for stroke and SCI trials22, 23. A group of editors for some 400 journals have already set standards for publication of clinical trials via the CONSORT (Consolidated Reporting of Trials) guidelines 24, 25 and, similarly, journal editors are calling for improvements in the conduct and reporting of pre-clinical research 26. However, the CDE concept is being applied slowly in the preclinical arena. A parallel worldwide effort is being launched under the umbrella of the Minimum Information about a Biomedical and Biological Investigation (MIBBI) project27. Working groups associated with various organizations and ad hoc groups have developed reporting standards. Perhaps the most widely used is the Minimum Information About a Microarray Experiment (MIAME) 28. Similar approaches are being encouraged via the ARRIVE guideline (Animals in Research: Reporting in Vivo Experiments) 29 and the CAMARADES initiative (http://www.camarades.info/) for experimental models of multiple sclerosis, traumatic brain injury (TBI) and stroke 30-32 . Finally, reporting standards can help reviewers evaluate and critique grants and manuscripts. It is worth noting that while reporting standards encourage the use of best practices by focusing attention on critical concepts in a particular experimental domain, they are not to be confused with experimental practice standards. Preclinical research requires innovation that might be hampered if only existing models or assessment methods were allowed. The adoption of a reporting standard not only improves transparency of research and encourages the use of best practices, it has the additional benefit of facilitating the aggregation and interrogation of large data sets in a given domain by annotating data and metadata using standardized terminology33. The number of publications each year already exceeds the capacity of individuals to find, read, and absorb them, even in relatively small research areas such as SCI. It is also difficult for researchers to compare variables across studies due to the lack of consistency in reporting experimental design parameters. Consequently, to ensure that valuable data are not lost or needlessly duplicated, these need to be collected into user-friendly knowledge bases. Moreover, as MIASCI aims to reduce bias and thereby enhance the predictive value of experimental SCI modelling, the number of animals needed to verify/falsify a scientific hypothesis could be reduced. Such an effort is in line with the “3R” (Replacement, Refinement and Reduction) initiative to increase animal welfare 34 and reduce waste in biomedical research 35, 36. To begin to address the problems outlined above, an international group of scientists studying SCI have worked collaboratively to develop a draft standard, termed Minimum Information about a Spinal Cord Injury experiment (MIASCI). Methods and Results: In October 2012 a three day workshop, entitled “Growth Cones and Axon Regeneration: Entering The Age of Informatics” was held in New Orleans. The thirty-five participants (listed in appendix A) spent substantial time in small working groups developing lists to describe important information relating to the performance of SCI experiments; i.e., the “metadata” concerning these experiments. Following the meeting, the documentation from these discussions was collated and circulated to the meeting’s advisory group for further review. A draft MIASCI checklist was assembled based on the guidelines recommended by the MIBBI project 27. 5


Page 6 of 17

6

The draft MIASCI was presented at four international meetings to obtain feedback from the SCI community 37-40. Finally, an online poll was conducted to obtain specific feedback concerning the importance of individual items in the checklist. Seventy-six SCI experts (of 125 invited to participate) from the global SCI research community participated in this poll. Thirty-four percent of the participants had more than 10 years experience in the SCI field and 24% had 4-10 years of experience. On December 11, 2013, a draft MIASCI was listed at the BioSharing portal (http://biosharing.org/bsg-000541), the current host of MIBBI checklists, and the MIASCI checklist (version 0.8) was posted at SourceForge (https://sourceforge.net/projects/miasci), a resource for open source software development and distribution. The 1.0 version was posted on 4/14/2014 and is attached as appendix B. MIASCI Data Elements Typical Minimum information standards (MIS) strive to minimize the number of required data elements to increase the likelihood that investigators will provide essential information. The average MIS has about 50 required data elements. Because the design and analysis of SCI experiments varies widely, the draft MIASCI has approximately 250 required data elements. However, most SCI studies only cover a narrow range of these elements and for a given study the number of applicable data elements from the MIASCI is likely to be 100 or less. The draft MIASCI has 11 major sections: investigator, organism, surgery, perturbagen, cell transplantation, biomaterials, histology, immunohistochemisty, imaging, behavior, and data analysis and statistics. The section on organism covers important information such as animal source, strain and congenic status. Correct identification of strain and details about congenic status is increasingly recognized as essential information. Different mouse strains show different response to injuries and recovery patterns after SCI and optic nerve crush 41-43. The same rat strain from two different regional suppliers of the same commercial vendor can yield different outcomes in SCI experiments 44. Thus, the organism section also covers information about housing that has proven critical to the outcome of SCI experiments, such as animal batching, environmental enrichment and light/dark cycle 10. Animal batching (randomized, randomized block, etc) can be complicated 45, especially when working with transgenic mice that might be difficult to produce in large numbers. Nonetheless, reporting how this is managed is important. Details about control groups (littermates, congenic status, etc.) should also be documented. The surgery and behavior sections include whether the surgeon/s are blinded to treatment group (concealed allocation), the type of injury and device used to inflict it including whether compression was maintained following impact and for how long as well as data elements regarding drugs (e.g., anesthetics, analgesics, antibiotics) given to animals and hydration. Based on the recommendations of Landis et al. 17 those sections also cover animal batching methods, power calculation methods and estimation of effect size and details about whether observers were blinded to the experimental intervention. Small sample size in biological studies is a general problem 14 but can be a special problem in SCI research, since animal experiments are especially time consuming and expensive. Therefore it is critical for scientists to consider and report this aspect of their work. In the behavior 6


Page 7 of 17

7 section, special attention is paid to collecting important metadata about the widely used “BBB test” 46 , “BMS test” 41 and various gait analysis methods. A major focus of SCI research is in evaluating the ability of agents to improve recovery after injury. The drug discovery field has adopted the term “perturbagen” to refer to small molecules, peptides, antibodies, oligonucleotides, etc., that alter a biological process by interfering with one or more molecular targets. Common perturbagens used in the SCI field are FDA approved drugs, chemical compounds, naturally occurring bioactive agents, siRNAs, shRNAs and cDNAs. The route (oral; iv; SC, minipump etc) and other aspects (time since injury, dose/s) of administration of the perturbagen needs to be documented. The Minimum Information About a Cellular Assay (MIACA) project (http://miaca.sourceforge.net) proposed a standard that included data elements about perturbagens such as vendor, catalogue number, stock concentration, storage and solvent. MIACA also covers experiments using viruses (type, titer). In accord with best practices in MIBBI and ontology development we have chosen to reuse relevant sections of MIACA to describe perturbagen use in MIASCI. The cell transplantation section requests information about cell source, isolation and purification methods, batch and passage inspired by Good Laboratory Practice/Good Manufacturing Practice standards. Additional information about growth factors and differentiation methods is included, as is information about any immunosuppression methods or use of supporting growth factors administered at the time of cellular delivery. In addition, the time since injury, site, route and volume of introduction are also required as well as the numbers of cells and numbers of times the cells are delivered and over what duration. Biomaterials are also covered, as they are commonly used in SCI experiments. Domain experts recommended that details about composition, mechanical properties, manufacturer and manufacturing methods be collected along with details about release kinetics, as well as mode and rate of metabolism, if the material is used to deliver a compound or biologic and whether any safety data are available regarding biodistribution after introduction. Histology, Immunohistochemistry and Imaging are three highly interrelated areas often used in evaluating the results of SCI experiments. The histology section of MIASCI deals with fixation, tissue processing and axonal tracing methods. The immunohistochemistry section is devoted to collecting information about antibodies used in the research project. The Journal of Comparative Neurology has set a very high bar for describing antibodies and verifying the specificity of antibody labeling 47. Most other journals do not have such high standards so better documentation of antibodies and their specificity remains a major concern 48 (source and catalogue number, at least, are essential, batch information is very desirable). The Neuroscience Information Framework (NIF) has an antibody registry (www.antibodyregistry.org), which provides unique identifiers for antibodies, including those available from about 200 vendors. MIASCI will use these identifiers, and will link to the NIF search tool to facilitate data entry into MIASCI. Basic information about the imaging platform is requested, especially information about image acquisition and analysis software and settings, as well as the specific counting / measurement methods used 17. Software developers and computational biologists have discussed the critical importance of documenting software algorithms and settings 49, 50 51. This includes archiving exact versions of programs used and version control of all custom scripts. When this logic is applied to image analysis, it requires documentation of software versions and settings, optical filters and software filters, such as 7


Page 8 of 17

8 thresholds, used during image acquisition and analysis. We hope that the MIASCI will encourage the use of these imaging “best practices”. The data analysis and statistics section is relatively brief but covers concepts related to blinding of investigators, the kinds of technical and biological replicates used, prospective analysis plans and the statistical tests performed, normalization schemes and positive and negative controls. These data elements are deemed critical by the SCI domain experts and are common recommendations in standards for life science research 20 . An inevitable limitation is that a MIASCI statement relies on good faith and therefore cannot detect nor prevent intentionally false statements. However, the utility of MIASCI could be tested experimentally, for example by a prospective study comparing relevant publications before and after inauguration of the MIASCI standard. MIASCI acceptance and integration could be measured by analysing whether experimental characterization according to the MIASCI statement is increasing. MIASCI efficacy could be investigated by determining whether the precision of the primary outcome measure effect size increased after inauguration of the MIASCI standard. Summary: The Minimum Information about a Spinal Cord Injury experiment (MIASCI) draft standard has been proposed to capture SCI experimental details including the investigator, organism, behavior, surgery, perturbagens, histology, immunohistochemistry, imaging, biomaterials, cell transplantation and data analysis. MIASCI provides a basis for establishing Good laboratory Practice in the modeling of SCI. This first version of MIASCI will require modifications and further development as new methodologies are applied to the study and treatment of SCI. In some cases simply requiring the use of other standards, such as MIAME or Minimum Information about an RNA-Seq experiment, will be appropriate. In other cases, however, expanding or developing a new section may be needed. At present the biomaterials section is minimal and there is no coverage of some molecular techniques, such as in situ hybridization or real-time PCR. As scientists, reviewers and editors use the MIASCI when reporting SCI studies, this should not only improve reporting but also promote the adoption of best practices such as randomization of animals to treatment groups, appropriate use of power analysis and the blinding of scientists to treatment conditions. To facilitate the adoption of MIASCI an overall framework, including an ontology and simple-to-use annotation tools, is being built and will be freely available for data annotation and submission. An important benefit of MIASCI adoption is that it will greatly facilitate the population of domainspecific databases such as NIF, Regenbase37 , Adam Ferguson’s SCI Database 52, 53, Barbara Grimpe’s SCI text mining initiative 54, the University of Dusseldorf Center for Neuronal Regeneration’s SCI Database 55 and the CAMARADES project on meta-analysis of animal studies 30, 32, 36 . Thus, establishment of transparent reporting standards in preclinical SCI research should facilitate experimental accuracy and lab-to-lab reproducibility, helping to speed up the development of novel therapeutic approaches to SCI.

Acknowledgments: The MIASCI was developed with the assistance of many people. It was inspired by the MIAME microarray reporting standard, the MIBBI Project, and the BioAssay Ontology Project. The original idea for MIASCI emerged while planning an international meeting in 2012 on axon growth and regeneration supported by the NIH and the Japan Society for the Promotion of Sciences (JSPS). Like MIAME and other reporting standards, the MIASCI is a grass8

Journal of Neurotrauma Minimum Information About a Spinal Cord Injury Experiment (MIASCI) – a proposed reporting standard for spinal cord injury experiments (doi: 10.1089/neu.2014.3400) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof. Page 9 of 17

9

roots movement and has depended on the pro bono work of stakeholders as well as support from NIH (HD057632, NS080145, U01HL111561) and the Miami Project to Cure Paralysis. Many of the papers on reproducibility were introduced to us by Carol Goble’s keynote talk at ISMB/ECCB 2013 Berlin 56.

9


Page 10 of 17

10 References 1. Sterling, T.D. (1959). Publication Decisions and Their Possible Effects on Inferences Drawn from Tests of Significance - or Vice Versa. Journal of the American Statistical Association 54, 30-34. 2. Cohen, J. (1962). Statistical Power of Abnormal-Social Psychological-Research - a Review. Journal of Abnormal Psychology 65, 145-&. 3. Cohen, J. (1994). The Earth Is Round (P-Less-Than.05). American Psychologist 49, 997-1003. 4. Prinz, F., Schlange, T. and Asadullah, K. (2011). Believe it or not: how much can we rely on published data on potential drug targets? Nat Rev Drug Discov 10, 712. 5. Begley, C.G. and Ellis, L.M. (2012). Drug development: Raise standards for preclinical cancer research. Nature 483, 531-533. 6. Sharp, K., Yee, K.M. and Steward, O. (2012). A re-assessment of the effects of treatment with an epidermal growth factor receptor (EGFR) inhibitor on recovery of bladder and locomotor function following thoracic spinal cord injury in rats. Exp Neurol 233, 649-659. 7. Watzlawick, R., Sena, E.S., Dirnagl, U., Brommer, B., Kopp, M.A., Macleod, M.R., Howells, D.W. and Schwab, J.M. (2014). Effect and Reporting Bias of RhoA/ROCK-Blockade Intervention on Locomotor Recovery After Spinal Cord Injury: A Systematic Review and Meta-analysis. JAMA Neurol 71, 91-99. 8. Antonic, A., Sena, E.S., Lees, J.S., Wills, T.E., Skeers, P., Batchelor, P.E., Macleod, M.R. and Howells, D.W. (2013). Stem cell transplantation in traumatic spinal cord injury: a systematic review and meta-analysis of animal studies. PLoS Biol 11, e1001738. 9. Steward, O., Zheng, B. and Tessier-Lavigne, M. (2003). False resurrections: distinguishing regenerated from spared axons in the injured central nervous system. J Comp Neurol 459, 1-8. 10. Fouad, K., Hurd, C. and Magnuson, D.S. (2013). Functional testing in animal models of spinal cord injury: not as straight forward as one would think. Front Integr Neurosci 7, 85. 11. Weishaupt, N., Krajacic, A. and Fouad, K. (2013). Lipopolysaccharide can induce errors in anatomical measures of neuronal plasticity by increasing tracing efficacy. Neurosci Lett 556, 181-185. 12. Nieuwenhuis, S., Forstmann, B.U. and Wagenmakers, E.J. (2011). Erroneous analyses of interactions in neuroscience: a problem of significance. Nat Neurosci 14, 1105-1107. 13. Burke, D.A., Whittemore, S.R. and Magnuson, D.S. (2013). Consequences of common data analysis inaccuracies in CNS trauma injury basic research. J Neurotrauma 30, 797-805.

10


Page 11 of 17

11 14. Button, K.S., Ioannidis, J.P., Mokrysz, C., Nosek, B.A., Flint, J., Robinson, E.S. and Munafo, M.R. (2013). Power failure: why small sample size undermines the reliability of neuroscience. Nat Rev Neurosci 14, 365-376. 15. Johnson, V.E. (2013). Revised standards for statistical evidence. Proc Natl Acad Sci U S A 110, 19313-19317. 16. Kwon, B.K., Okon, E.B., Tsai, E., Beattie, M.S., Bresnahan, J.C., Magnuson, D.K., Reier, P.J., McTigue, D.M., Popovich, P.G., Blight, A.R., Oudega, M., Guest, J.D., Weaver, L.C., Fehlings, M.G. and Tetzlaff, W. (2011). A grading system to evaluate objectively the strength of pre-clinical data of acute neuroprotective therapies for clinical translation in spinal cord injury. J Neurotrauma 28, 1525-1543. 17. Landis, S.C., Amara, S.G., Asadullah, K., Austin, C.P., Blumenstein, R., Bradley, E.W., Crystal, R.G., Darnell, R.B., Ferrante, R.J., Fillit, H., Finkelstein, R., Fisher, M., Gendelman, H.E., Golub, R.M., Goudreau, J.L., Gross, R.A., Gubitz, A.K., Hesterlee, S.E., Howells, D.W., Huguenard, J., Kelner, K., Koroshetz, W., Krainc, D., Lazic, S.E., Levine, M.S., Macleod, M.R., McCall, J.M., Moxley, R.T., 3rd, Narasimhan, K., Noble, L.J., Perrin, S., Porter, J.D., Steward, O., Unger, E., Utz, U. and Silberberg, S.D. (2012). A call for transparent reporting to optimize the predictive value of preclinical research. Nature 490, 187-191. 18. Vesterinen, H.M., Sena, E.S., Egan, K.J., Hirst, T.C., Churolov, L., Currie, G.L., Antonic, A., Howells, D.W. and Macleod, M.R. (2014). Meta-analysis of data from animal studies: a practical guide. J Neurosci Methods 221, 92-102. 19. Lazic, S.E. and Essioux, L. (2013). Improving basic and translational science by accounting for litter-to-litter variation in animal models. BMC Neurosci 14, 37. 20. Henderson, V.C., Kimmelman, J., Fergusson, D., Grimshaw, J.M. and Hackam, D.G. (2013). Threats to validity in the design and conduct of preclinical efficacy studies: a systematic review of guidelines for in vivo animal experiments. PLoS Med 10, e1001489. 21. Alsheikh-Ali, A.A., Qureshi, W., Al-Mallah, M.H. and Ioannidis, J.P. (2011). Public availability of published research data in high-impact journals. PLoS One 6, e24357. 22. Saver, J.L., Warach, S., Janis, S., Odenkirchen, J., Becker, K., Benavente, O., Broderick, J., Dromerick, A.W., Duncan, P., Elkind, M.S., Johnston, K., Kidwell, C.S., Meschia, J.F., Schwamm, L., National Institute of Neurological, D. and Stroke Stroke Common Data Element Working, G. (2012). Standardizing the structure of stroke clinical and epidemiologic research data: the National Institute of Neurological Disorders and Stroke (NINDS) Stroke Common Data Element (CDE) project. Stroke 43, 967-973. 23. Biering-Sorensen, F., Charlifue, S., Devivo, M.J., Grinnon, S.T., Kleitman, N., Lu, Y. and Odenkirchen, J. (2011). Incorporation of the International Spinal Cord Injury Data Set elements into the National Institute of Neurological Disorders and Stroke Common Data Elements. Spinal Cord 49, 60-64.

11


Page 12 of 17

12 24. Boutron, I., Moher, D., Altman, D.G., Schulz, K.F., Ravaud, P. and Group, C. (2008). Extending the CONSORT statement to randomized trials of nonpharmacologic treatment: explanation and elaboration. Ann Intern Med 148, 295-309. 25. Moher, D., Hopewell, S., Schulz, K.F., Montori, V., Gotzsche, P.C., Devereaux, P.J., Elbourne, D., Egger, M., Altman, D.G. and Consolidated Standards of Reporting Trials, G. (2010). CONSORT 2010 Explanation and Elaboration: Updated guidelines for reporting parallel group randomised trials. J Clin Epidemiol 63, e1-37. 26. Hoke, A. (2013). Experimental neurology and state of preclinical research. Exp Neurol 239, A1. 27. Taylor, C.F., Field, D., Sansone, S.A., Aerts, J., Apweiler, R., Ashburner, M., Ball, C.A., Binz, P.A., Bogue, M., Booth, T., Brazma, A., Brinkman, R.R., Michael Clark, A., Deutsch, E.W., Fiehn, O., Fostel, J., Ghazal, P., Gibson, F., Gray, T., Grimes, G., Hancock, J.M., Hardy, N.W., Hermjakob, H., Julian, R.K., Jr., Kane, M., Kettner, C., Kinsinger, C., Kolker, E., Kuiper, M., Le Novere, N., LeebensMack, J., Lewis, S.E., Lord, P., Mallon, A.M., Marthandan, N., Masuya, H., McNally, R., Mehrle, A., Morrison, N., Orchard, S., Quackenbush, J., Reecy, J.M., Robertson, D.G., Rocca-Serra, P., Rodriguez, H., Rosenfelder, H., Santoyo-Lopez, J., Scheuermann, R.H., Schober, D., Smith, B., Snape, J., Stoeckert, C.J., Jr., Tipton, K., Sterk, P., Untergasser, A., Vandesompele, J. and Wiemann, S. (2008). Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 26, 889-896. 28. Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C., Gaasterland, T., Glenisson, P., Holstege, F.C., Kim, I.F., Markowitz, V., Matese, J.C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J. and Vingron, M. (2001). Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29, 365-371. 29. Kilkenny, C., Browne, W.J., Cuthill, I.C., Emerson, M. and Altman, D.G. (2010). Improving bioscience research reporting: the ARRIVE guidelines for reporting animal research. PLoS Biol 8, e1000412. 30. Sena, E., van der Worp, H.B., Howells, D. and Macleod, M. (2007). How can we improve the pre-clinical development of drugs for stroke? Trends Neurosci 30, 433-439. 31. Howells, D.W., Sena, E.S. and Macleod, M.R. (2014). Bringing rigour to translational medicine. Nat Rev Neurol 10, 37-43. 32. Crossley, N.A., Sena, E., Goehler, J., Horn, J., van der Worp, B., Bath, P.M.W., Macleod, M. and Dirnagl, U. (2008). Empirical evidence of bias in the design of experimental stroke studies - A metaepidemiologic approach. Stroke 39, 929-934. 33. Schurer, S.C., Vempati, U., Smith, R., Southern, M. and Lemmon, V. (2011). BioAssay Ontology Annotations Facilitate Cross-Analysis of Diverse High-Throughput Screening Data Sets. Journal of Biomolecular Screening 16, 415-426.

12


Page 13 of 17

13 34. van Luijk, J., Cuijpers, Y., van der Vaart, L., de Roo, T.C., Leenaars, M. and Ritskes-Hoitinga, M. (2013). Assessing the application of the 3Rs: a survey among animal welfare officers in The Netherlands. Lab Anim 47, 210-219. 35. Macleod, M.R., Michie, S., Roberts, I., Dirnagl, U., Chalmers, I., Ioannidis, J.P., Al-Shahi Salman, R., Chan, A.W. and Glasziou, P. (2014). Biomedical research: increasing value, reducing waste. Lancet 383, 101-104. 36. Chalmers, I., Bracken, M.B., Djulbegovic, B., Garattini, S., Grant, J., Gulmezoglu, A.M., Howells, D.W., Ioannidis, J.P. and Oliver, S. (2014). How to increase value and reduce waste when research priorities are set. Lancet 383, 156-165. 37. Lemmon, V.P. (2013). Functional genomics and spinal cord injury. In: International Spinal Research Network Meeting: London, UK. 38. Lemmon, V.P., Ferguson, A.R., Popovich, P.G. and Bixby, J.L. (2013). A Draft Minimal Information Standard for Spinal Cord Injury Experiments. In: National Neurotrauma Symposium: Nashville, TN. 39. Lemmon, V.P., Ferguson, A.R., Popovich, P.G., Snow, D.M., Mason, C., Igarashi, M., Xu, X.-M., Beattie, C. and Bixby, J.L. (2013). A Minimal Information Standard for Spinal Cord Injury Experiments. In: 3rd International Neural Regeneration Symposium: Shenyang, China. 40. Lemmon, V.P., Ferguson, A.R., Popovich, P.G., Snow, D.M., Mason, C., Igarashi, M., Xu, X.-M., Beattie, C. and Bixby, J.L. (2013). A Minimal Information Standard for Spinal Cord Injury Experiments. In: British Society for Developmental Biology - Axon Guidance and Regeneration: Aberdeen, UK. 41. Basso, D.M., Fisher, L.C., Anderson, A.J., Jakeman, L.B., McTigue, D.M. and Popovich, P.G. (2006). Basso Mouse Scale for locomotion detects differences in recovery after spinal cord injury in five common mouse strains. J Neurotrauma 23, 635-659. 42. Kigerl, K.A., McGaughy, V.M. and Popovich, P.G. (2006). Comparative analysis of lesion development and intraspinal inflammation in four strains of mice following spinal contusion injury. J Comp Neurol 494, 578-594. 43. Cui, Q., Hodgetts, S.I., Hu, Y., Luo, J.M. and Harvey, A.R. (2007). Strain-specific differences in the effects of cyclosporin A and FK506 on the survival and regeneration of axotomized retinal ganglion cells in adult rats. Neuroscience 146, 986-999. 44. Bunge, M.B. and Pearse, D.D. (2012). Response to the report, "A re-assessment of a combinatorial treatment involving Schwann cell transplants and elevation of cyclic AMP on recovery of motor function following thoracic spinal cord injury in rats". Exp Neurol 233, 645648. 45. Keppel, G. and Wickens, T.D. (2004). Design and Analysis : a Researcher's Handbook. Pearson Prentice Hall: Upper Saddle River, N.J. 13


Page 14 of 17

14 46. Basso, D.M., Beattie, M.S. and Bresnahan, J.C. (1995). A sensitive and reliable locomotor rating scale for open field testing in rats. J Neurotrauma 12, 1-21. 47. Saper, C.B. (2005). An open letter to our readers on the use of antibodies. J Comp Neurol 493, 477-478. 48. Rhodes, K.J. and Trimmer, J.S. (2006). Antibodies as valuable neuroscience research tools versus reagents of mass distraction. J Neurosci 26, 8017-8020. 49. Peng, R.D. (2011). Reproducible research in computational science. Science 334, 12261227. 50. Sandve, G.K., Nekrutenko, A., Taylor, J. and Hovig, E. (2013). Ten simple rules for reproducible computational research. PLoS Comput Biol 9, e1003285. 51. Nekrutenko, A. and Taylor, J. (2012). Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nat Rev Genet 13, 667-672. 52. Ferguson, A.R., Irvine, K.A., Gensel, J.C., Nielson, J.L., Lin, A., Ly, J., Segal, M.R., Ratan, R.R., Bresnahan, J.C. and Beattie, M.S. (2013). Derivation of multivariate syndromic outcome metrics for consistent testing across multiple models of cervical spinal cord injury in rats. PLoS One 8, e59712. 53. Nielson JL, Guandique CF, Liu AW, Burke DA, Lash AT, Moseanko R, Hawbecker S, Strand SC, Zdunowski S, Irvine K-A., Brock JH, Rosenzweig ES, Nout YS, Gensel JC, Anderson KD, Segal MR, Magnuson DSK, Whittemore SR, McTigue DM, Popovich PG, Rabchevsky AG, Scheff SW, Steward O, Courtine G, Edgerton VR, Tuszynski MH, Beattie MS, Bresnahan JC and AR, F. (in press). Development of a Database for Translational Spinal Cord Injury Research. J Neurotrauma. 54. Ries, A., Goldberg, J.L. and Grimpe, B. (2007). A novel biological function for CD44 in axon growth of retinal ganglion cells identified by a bioinformatics approach. J Neurochem 103, 1491-1505. 55. Brazda, N., Kruse, F., Kruse, M., Kirchhoffer, T., Klinger, R., Cimiano, P. and Muller, H.W. (2013). The CNR preclinical database for knowledge management in spinal cord injury research. In: Society for Neuroscience: San Diego, CA. 56. Goble, C. (2013). Results may vary; reproducibility, open science and all that jazz. In: International Conference on Intelligent Systems for Molecular Biology: Berlin, Germany.

14

Journal of Neurotrauma Information About a Spinal Cord Injury Experiment (MIASCI) – a proposed reporting standard for spinal cord injury experiments (doi: 10.1089/neu.2 as been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ fro

Page 15 of 17

15

Growth Cones and Axon Regeneration: Entering The Age of Informatics A 3-day workshop sponsored by NINDS, NICHD and the Japan Society for the Promotion of Sciences (JSPS). New Orleans, LA, October 10-12, 2012

Co-Organizers: Michihiro Igarashi, Neurochemistry and Molecular Cell Biology, Niigata University, Niigata, Japan, 951-8510 Vance P. Lemmon, Miami Project to Cure Paralysis, Neurological Surgery, University of Miami, Miami, FL, USA, 33136

Participants: Saminda W. Abeyruwan, Computer Sciences, University of Miami, Miami, FL, USA, 33146, Christine E. Beattie, Neuroscience, Ohio State University, Columbus, OH, USA, 43210 John L. Bixby, Miami Project to Cure Paralysis, Molecular and Cellular Pharmacology, Neurological Surgery, University of Miami, Miami, FL, USA, 33136 Alison Callahan, Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA, 94305 Adam R. Ferguson, Brain and Spinal Injury Center, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA, 94110 Paul Forscher, Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, USA, 06511 Yoshio Goshima, Molecular Pharmacology & Neurobiology, Yokohama City University, Yokohama, Japan, 236-0004 Benjamin J. Harrison, Kentucky Spinal Cord Injury Research Center, University of Louisville, Louisville, KY, USA, 40292 Zhigang He, F. M. Kirby Neurobiology Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA, 02115 Tatsumi Hirata, Division of Brain Function, National Institute of Genetics, Mishima, Shizuoka, Japan, 411-8540 Ken Kadoya, Neurosciences, University of California, San Diego, San Diego, CA, USA, 92093 Hiroyuki Kamiguchi, Laboratory for Neuronal Growth Mechanisms, RIKEN Brain Science Institute, Wako, Saitama, Japan, 351-0198 Mineko Kengaku, Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan, 606-8501 Laura A. Lowery, Biology, Boston College, Chestnut Hill, MA, USA, 02467 Shweta Mandrekar-Colucci, Center for Brain and Spinal Cord Repair, Department of Neuroscience, Ohio State University, Columbus, OH, USA, 43210 Carol A. Mason, Pathology and Cell Biology, Neuroscience, and Ophthalmic Science, Columbia University, New York, NY, USA, 10032 Nassir Mokarram, The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA, 30332

15


Page 16 of 17

16 Takeshi Nakamura, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba, USA, 289-0022 Takashi Namba, Cell Pharmacology, Nagoya University, Nagoya, Japan, 466-8550 Mariko Nishibe, Molecular Neuroscience, Osaka University, Osaka, Japan, 565-0871 Izumi Oinuma, Laboratory of Molecular Neurobiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan, 606-8501 Phillip G. Popovich, Center for Brain and Spinal Cord Repair, Ohio State University, Columbus, OH, USA, 43210 Miguel Santiago-Medina, Neuroscience, University of Wisconsin, Madison, WI, USA, 53706 Yohei Shinmyo, Developmental Neurobiology, Kumamoto University, Kumamoto, Japan, 860-8556, Diane M. Snow, Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, USA, 40636 Oswald Steward, Reeve-Irvine Research Center, University of California, Irvine, Irvine, CA, USA, 92697 Jeffery L. Twiss, Biological Sciences, University of South Carolina, Columbus, SC, USA, 29208 Ubbo Visser, Computer Science, University of Miami, Miami, FL, USA, 33146 Trent A. Watkins, Neuroscience, Genentech, Inc., South San Francisco, CA, USA, 94080 Xiao-Ming Xu, Stark Neurosciences Research Institute, Indiana University, Indianapolis, IN, USA, 46202 Michisuke Yuzaki, Neurophysiology, Keio University, Tokyo, Japan, 160-8582 Binhai Zheng, Neurosciences, University of California San Diego, San Diego, CA, USA, 92093

16

Journal of Neurotrauma Minimum Information About a Spinal Cord Injury Experiment (MIASCI) – a proposed reporting standard for spinal cord injury experiments (doi: 10.1089/neu.2014.3400) This article has been peer-reviewed and accepted for publication, but has yet to undergo copyediting and proof correction. The final published version may differ from this proof. Page 17 of 17

17

Workshop participants

17


MIASCI: TAB 1 Minimum Information About a Spinal Cord Injury experiment TAB 1 Version 1.0 14-Apr-14 MIASCI has approximately 280 elements but many SCI studies only cover a small fraction of the elments. For example, most studies do not invlove, large chemical libraries, siRNA libraries, stem cells or biomaterials. So the number of requried elemets will vary substantially by study. First Name M.I. Last Name Lead Authors

Department

University

City

State Country ZIP CODE

Miami

FL

USA

33136

P.

Lemmon

Miami Project to Cure Paralysis, Neurological Surgery University of Miami

Adam R. Phillip G. Xiao-Ming

Ferguson Popovich Xu

Brain and Spinal Injury Center, Department of Neurological Surgery Center for Brain and Spinal Cord Repair Stark Neurosciences Research Institute

University of California, San Francisco San Francisco CA Ohio State University Columbus OH Indiana University Indianapolis IN

USA USA USA

94110 43210 46202

Diane Michihiro Christine

M.

University of Kentucky Lexington Niigata University Niigata Ohio State University Columbus

OH

USA Japan USA

40636 951-8510 43210

John

L.

Bixby

Spinal Cord and Brain Injury Research Center Neurochemistry and Molecular Cell Biology Neuroscience Miami Project to Cure Paralysis, Molecular and Cellular Pharmacology, Neurological Surgery

KY

E.

Snow Igarashi Beattie

University of Miami

Miami

FL

USA

33136

MIASCI Consortium Saminda W. Abeyruwan

Computer Sciences

University of Miami

Miami

FL

USA

33146

Michael John

Beattie Bethea

Neurological Surgery Biology

USA USA

94110 19104

Bradke

Axon Growth and Regeneration

Vance

Frank

S. R.

University of California, San Francisco San Francisco CA Drexel University Philadelphia PA German Center for Neurodegenerative Diseases Bonn

Germany

D-53175


MIASCI: TAB 1

Jacqueline Mary

C. B.

Bresnahan Bunge

Alison

Callahan

Neurological Surgery Miami Project to Cure Paralysis Stanford Center for Biomedical Informatics Research

Samuel

David

Centre for Research in Neuroscience

University of California, San Francisco San Francisco CA University of Miami Miami FL Stanford University

Stamfprd Montreal

CA USA Queb ec Canada

Crawley

WA

Cambridge

Sarah

A.

Dunlop

Experimental & Regenerative Neurosciences

McGill University University of Western Australia

James

W.

Fawcett

Centre for Brain Repair

Cambridge University

Michael

G.

Fehlings

Neurosurgery

Fischer Forscher Giger

Neurobiology and Anatomy Molecular, Cellular, and Developmental Biology Cell and Debelopmental Biology

Yoshio

Goshima

Molecular Pharmacology & Neurobiology

Barbara

Grimpe

Applied Neurobiology

Theo

Hagg

Department of Biomedical Sciences Anatomy & Neurobiology, Neurosurgery, Neurology and Physical Medicine & Rehabilitation

Itzhak Paul Roman

J.

Edward

D.

Hall

Benjamin

J.

Harrison

Alan

R.

Harvey

Cheng

He

Zhigang

He

USA USA

94110 33136 94305 H3G 1A4

Australia

06009

United Kingdom

CB2 0PY

University of Toronto Drexel University College of Medicine

Toronto

Ontari o Canada

Philadelphia

PA

USA

19129

Yale University University of Michigan Yokohama City University Graduate School of Medicine University Medical Center Düsseldorf East Tennessee State University

New Haven Ann Arbor

CT MI

USA USA

00651 48109

Yokohama

Japan

236-0004

Düsseldorf

Germany

40225

TN

USA

37614

KY

USA

40536

Louisville

KY

USA

40292

Crawley

WA

Australia

06009

Johnson City

University of Kentucky Lexington

Kentucky Spinal Cord Injury Research Center University of Louisville The University of Anatomy, Physiology and Human Biology, Western Australia Second Military Medical Neurobiology University F. M. Kirby Neurobiology Center, Boston Children¹s Hospital, Harvard Medical School

Shanghai Boston

M5T2S8

China MA

USA

02115


MIASCI: TAB 1

Tatsumi Ahmet Claire

E.

Andres Anjana Ken Hiroyuki Mineko Jeffery Brian Jae Daniel Shao-Jun Laura

National Institute of Genetics Johns Hopkins Hoke Neurology and Neuroscience University Universtiy of Texas Hulsebosch Neuroscience and Cell Biology Medical Branch Johns Hopkins Hurtado Neurology University Worcester Polytechnic Jain Biomedical Engineering Institute University of California, Kadoya Neurosceinces San Diego RIKEN Brain Science Kamiguchi Laboratory for Neuronal Growth Mechanisms Institute Kengaku Institute for Integrated Cell-Material Sciences Kyoto University Kocsis Neurology Yale University University of British Kwon Orthopaedics Columbia Lee Neurological Surgery University of Miami Liebl Neurological Surgery University of Miami The Academy of Military Medical Liu Department of Neurobiology Sciences Lowery Biology Boston College Center for Brain and Spinal Cord Repair, Mandrekar-Colucci Department of Neuroscience Ohio State University The City College of the City University of New Martin Physiology, Pharmacology & Neuroscience York Pathology and Cell Biology, Neuroscience, Mason and Ophthalmic Science Columbia University McTigue Neuroscience Ohio State University The Wallace H. Coulter Department of Georgia Institute of Mokarram Biomedical Engineering Technology Hirata

D. K. J.

A.

Shweta John

H.

Carol Dana

A. M.

Nassir

Division of Brain Function

Lawrence

D.

Moon

Wolfson Centre for Age-Related Diseases

Hans

W.

Muller

Neurology

Mishima

Shizu oka Japan

Baltimore

MD

USA

21205

Galveston

Texas USA

77555

Baltimore

MD

USA

21205

Worcester

MA

USA

01609

San Diego

92093

Wako Kyoto West Haven

CA USA Saita ma Japan Japan CT USA

351-0198 606-8501 06516

Vncouver Miami Miami

BC FL FL

Canada USA USA

V5Z 1M9 33136 33136

Beijing Chestnut Hill

MA

China USA

02467

Columbus

OH

USA

43210

New York

NY

USA

10031

New York Columbus

NY OH

USA USA

10032 43210

Atlanta

GA

USA

30332

King's College London, University of London London Heinrich-HeineUniversity Düsseldorf

411-8540

United Kingdom

SE1 1UL

Germany

D-40225


MIASCI: TAB 1 Tokyo University of Science Nagoya University Osaka Universtiy

Noda Nagoya Osaka

Kyoto University

Kyoto

Takeshi Takashi Mariko

Nakamura Namba Nishibe

Izumi

Oinuma

Martin

Oudega

Research Institute for Biomedical Sciences Cell Pharmacology Molecular Neuroscience Laboratory of Molecular Neurobiology, Graduate School of Biostudies Physical Medicine and Rehabilitation, Neurobiology, and Bioengineering

Pleasure

Neurology and Pediatrics

University of Pittsburgh Pittsburgh University of California, Davis Sacramento

Raisman Rasband Reier

Spinal Repair Unit, Institute of Neurology Neuroscience, Developmental Biology, andMolecular and Cellular Biology Neuroscience

University College London Baylor College of Medicine University of Florida

Santiago-Medina

Neuroscience

David

E.

Geoffrey Matt Paul

N. J.

Miguel Jan

M.

Schwab

Klinik und Poliklinik für Neurologie & Experimentelle Neurologie

Martin Yohei

E.

Schwab Shinmyo

Brain Research Institute Developmental Neurobiology

Silver Smith

Neurosciences Neuroscience

So

GHM Institute of CNS Regeneration

Jerry George

M.

Kwok-fai Michael

V.

Sofroniew

Stephen

M.

Strittmatter

Neurobiology Cellular Neuroscience, Neurodegeneration and Repair

Mark

H.

Tuszynski

Center for Neural Repair, Neurosciences

Jeffery Ubbo

L.

Twiss Visser

Biological Sciences Computer Sciences

Houston Gainesville

Japan

606-8501

PA

USA

15213

CA

USA

95718

United Kingdom

Cleveland Philadelphia

WC1N 3BG

TX FL

USA USA

77030 32610

WI

USA

53706

Germany Switzerla nd Japan

10117

Zurich Kumamoto

Jinan University Guangzhou University of Califorina, Los Angeles Los Angeles Yale University University of California, San Diego Universtiy of South Carolina University of Miami

289-0022 466-8550 565-0871

London

University of Wisconsin Madison Charité Universitätsmedizin Berlin Berlin University of Zurich Kumamoto University Case Western Reserve University Temple University

Chiba USA Japan Japan

OH PA

USA USA

CH-8057 860-8556 44106 19140

Guan gdong China CA

USA

90095

New Haven

CT

USA

06536

San Diego

CA

USA

92093

Colombus Miami

SC FL

USA USA

29208 33146


MIASCI: TAB 1

Trent

A.

Watkins

Wutian Sung Ok Michisuke

Wu Yoon Yuzaki

Binhai

Zheng

Fengquan

Zhou

Yimin

Zou

Neuroscience

Genentech, Inc. The University of Hong Anatomy Kong Molecular & Cellular Biochemistry Ohio State University Neurophysiology Keio University University of California Neurosciences San Diego Johns Hopkins Orthopaedic Surgery & Neuroscience University Neurobiology Section, Division of Biological University of California, Sciences San Diego

South San Francisco

CA

USA

Hong Kong Columbus Tokyo

OH

China USA Japan

San Diego

CA

USA

92093

Baltimore

MD

USA

21205

San Diego

CA

USA

92093

MIASCI Full Copyright Notice Copyright © MIASCI Standards Initiative (2013-2014). All Rights Reserved. This document and translations of it may be copied and furnished to others, and derivative works that comment on or otherwise explain it or assist in its implementation may be prepared, copied, published and distributed, in whole or in part, without restriction of any kind, provided that the above copyright notice and this paragraph are included on all such copies and derivative works. However, this document itself may not be modified in any way, such as by removing the copyright notice or references to the MIASCI Standards Initiative or other organizations, except as needed for the purpose of developing MIASCI Standards Initiative Recommendations in which case the procedures for copyrights defined in the MIASCI Document process must be followed, or as required to translate it into languages other than English. The limited permissions granted above are perpetual and will not be revoked by the MIASCI Standards Initiative or its successors or assigns. This document and the information contained herein is provided on an "AS IS" basis and THE MIASCI STANDARDS INITIATIVE DISCLAIMS ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO ANY WARRANTY THAT THE USE OF THE INFORMATION HEREIN WILL NOT INFRINGE ANY RIGHTS OR ANY IMPLIED WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. This copyright notice is adapted from the MIACI copyright notice: http://miaca.sourceforge.net/copyrightNotice.txt

94080 43210 160-8582


MIASCI: TAB 2 Minimum Information About a Spinal Cord Injury experiment TAB 2 Investigator Organization Name Address

Example

Notes

University of …

Person responsible or Corresponding Author Name should be of the person holding responsibility for the associated metadata and data

Name Affiliation

Dept. of

Stable contact information Globally-unique personal ID Date Purpose Keywords outcome variables

Such information should be one or more from the following list: email; telephone (plus international dialing code); postal address. Where available, please give a unique person identifier and the system of which it is part (e.g., ISNI, ResearcherID, etc.). Date of submission

free text free text free text


MIASCI: TAB 3 Minimum Information About a Spinal Cord Injury experiment TAB 3 Organism

Example

Binomial systematic name (genus and species) Phenotype Genotype How was genotype confirmed? Source/Vendor Organism Vendor Cat # Strain Number of Generations backcrossed Sex PubMed Reference het vs. homozygote propagation strategy Age at sacrifice

Mus musculus Hydrocephalus L1cam KO PCR Jackson 3120 B6;129S7-L1camtm1Sor/J >10 M/F PMID: 9580664 het het F vs. wt M 14 days/weeks/months

Housing Group vs. Single Light/Dark Cycle When tested relative to Light/Dark cycle Enrichment Exercise opportunities Food Supplemental nutrical

Notes

Group 12-12 if yes, details if yes, give details

toys, nestlets requried by IACUC, etc. repeated BBB testing?


MIASCI: TAB 4 Minimum Information About a Spinal Cord Injury experiment TAB 4 Surgery

Example

Anesthetics Systemic Anesthetics Anesthetic 1 Source catalogue number amount solvent delivery method Local Anesthetics Source catalogue number amount solvent delivery method Surgical details Concealed allocation: were experimenters blinded to treatments? Y/N Does the phenotype of a transgenic animal make its genetic status Y/N obvious? Injury Level Surgery duration min/hr Surgery time of day Batching method Timing Method of effect size calculation Method of power calculation Number of surgeons in project Injury Method

Cohen's d, eta squared, omega squared, Rsquared, etc.

Notes


MIASCI: TAB 4 Contusion Contusion Device Manufacture Contusion Device Model Contusion Device Modifications Contusion Device settings Contusion Device biomechanical results Severity mild/medium/severe Compression maintained following impact and if so, how long? seconds Note: Commonly used devices (Infinite Horizons, NYU, OSU) will have relevant questions: an example is the following NYU impactor biomechanical results Velocity Compression / displacement Force Hemisection If yes, provide details Neurochemical If yes, provide details Nerve crush If yes, provide details Compression If yes: compression force and duration If yes: residual compression and duration Vascular occlusion If yes, provide details Transection If yes, provide details Reporters Axon labeling method Post Surgery Care Hydration Solution volume delivery method frequency

Y/N Y/N Y/N Y/N Y/N Y/N


MIASCI: TAB 4

Antibiotics source catalogue number volume delivery method frequency Bladder expression Frequency Timing relative to behavioral testing Treatment Batching method / method of randomization Animal Attrition Exclusion criteria Were exclusion criteria established before the study was initiated Health Outcomes number of animals excluded for any reason why were animals excluded

coin toss, computer generated This is requried in clinical trials


MIASCI: TAB 5 Minimum Information About a Spinal Cord Injury experiment TAB 5 Perturbagen Adapted from MIACA 080404

Example http://miaca.sourceforge.net/copyrightNotice.txt http://miaca.sourceforge.net/

Perturbagen Name Perturbagen Type Perturbagen Sequence/Composition: of siRNA/shRNA; structure/’smile’/CHEBI if compound Perturbagen manufacturer Perturbagen Catalogue # Perturbagen Lot # Perturbagen Target Species: e.g. if siRNA Perturbagen Stock Concentration Perturbagen Solvent Solvent Final concentration Stock storage condition If perturbagen is a compound, is any information available about its biodistribution? if Perturbagen is part of a library Library Name Library Type Library Format Library manufacture Library Catalogue # Library Preparation Methodology Library Features if Perturbagen is virus: Virus Type Virus isotype Virus Titer Titration method Promoter driving protein/miRNA expression

cDNA, ORF, siRNA, shRNA, miRNA, morphilino, compound, bioactives,, single/pooled

Number of unique features (genes, compounds)


MIASCI: TAB 5 IRIS/2A peptide/Dual Promoter if Perturbagen is other stress/condition, details are specified in cell culture conditions of the respective treatment, e.g. temperature Transfection Reagents Individual reagents are often combined to make up the final Perturbagen [plasmid DNA, siRNA, etc.] Transfection Reagent Name Transfection Reagent manufacture Transfection Reagent catalogue # Transfection Reagent/Perturbagen ratio Reagent Volume Reagent Concentration if Transfection involves electroporation Electoporation device name Electroporation device manufacture model number Electroporation conditions (e.g. program number, volts, pulse duration, pulse number, pulse shape if Treatment involves cells from a transgenic animal, report on organism page Organism! If treatment involves a transplant, report details of cell preparation on the cell transplant page Cell transplant Timing of perturbagen delivery relative to injury Treatment Delivery Rate Location Method & route (i.p., i.v., minipump) Dosage (mg/kg)

report on organism page


MIASCI: TAB 5 acute / chronic convection based


Minimum Information About a Spinal Cord Injury experiment TAB 6 Cell Transplants Cell source Isolation and purification methods Batch Passage Cell Purity % How cell purity assessed Were GMP/GLP procedures used in cell production? Y/N When transplanted with respect to injury immunosupression Y/N if yes, what was used? drug dose timing

Examples

Cyclosporine A/MP, FK506, Cyclosporine A,Cyclophosphamide

Was a control graft performed if yes, what was used? Long term safety of graft tested? How were cells grown How were cells differentiated Transplant volume Injection device Number of cells transplanted Transp[lant volumn Transplant media Added growth factors and enzymes Site of administration relative to injury iv administration (tail vein) Devices

free text free text

free text

PBS/DMEM/ NT3/BDNF/insulin, include concentration and source details

Y/N gels, nanotubes


Minimum Information About a Spinal Cord Injury experiment TAB 7 Biomaterials Biomaterials Composition Manufacture if commercially obtained Modulus Is biomaterial degradable Mechanism of degradation Rate of degradation Degradation byproducts Were organic solvents used in fabrication if so, what kind of organic solvents were used Functional groups for modification with compounds? What kind of functional group Used for drug release if yes, what are drug release kinetics

Example

Y/N

Y/N Y/N Y/N

Notes


Minimum Information About a Spinal Cord Injury experiment TAB 8 Histology

Example

Microscope and acquisition details Fixation Method Method anesthetic Prerinse Buffer Volume Temperature Fixative Buffer Volume Temperature Tissue Processing Sectioning method Normalization method for shrinkage Lesion volume/size White matter/Gray matter Sparing

pump/gravity Y/N PBS 50 mls room temperature 4% paraformaldehyde PBS 200 mls room temperature cryostat/microtome/vibrotome

Axonal tracing methods Traditional tracer Genetic tracer Viral tracer Where tracer injected When tracer injected relative to injury Immunohistochemistry Characterization of injury?

fluorgold brainbow mice AAV8 mCherry Motor cortex 4 weeks after injury

Notes


Measures of sprouting Measures of regeneration Measures of spanning

Clearing method

Cell counts Method BABB, Clarity,

Y/N


Minimum Information About a Spinal Cord Injury experiment TAB 9 Immunohistochemistry Investigators are encouraged to use the NIF Antibody Registry http://antibodyregistry.org If you find your antibody in the NIF This provides unique identifiers and Antibody Registry and supply the many details about commonly used "antibody ID", we will pull all the rest of antibodies in neuroscience the information for you. Neurons identified Marker used

Y/N

Neurites identified Marker used

Y/N

Axons identified Marker used

Y/N

Dendrites identified Marker used

Y/N

Growth Cones identified Marker used

Y/N

Synapses identified Markers used

Y/N

Astrocytes identified Markers used

Y/N

Oligodendrocytes identified Markers used

Y/N

Schwann cells identified Markers used

Y/N


Microglia identified Markers used

NIF Antibody ID Antigen / Target Vendor Catalogue number Species Clonality lot # Y/N

Primary antibodies

if the user provides the NIF antibody ID, we auto fill the rest, except for lot#

mouse / rabbit / goat / donkey monoclonal / polyclonal


Minimum Information About a Spinal Cord Injury experiment TAB 10 Imaging Live Cell Imaging Immunostaining

Example Y/N Y/N widefield, confocal, 2-photon, lightsheet DIC, phase, fluorescence, FRET, FLIM,

Imaging Format: Imagining method: Microscope Manufacture Microscope Name Microscope model Were constant image acquisition standards used Y/N Camera Manufacture Camera type Camera Model Pixel binning Microscope Incubator Incubator Manufacture Incubator Model Temperature Nominal CO2 Percentage Humidified Temperature of objective controlled

Y/N Y/N

Imaging # observations / unit time Observer blinded to treatment? Imaging of Live or Dead cells Image Analysis Software Vendor

how long was shutter open Y/N

Notes


Software Package Name Software Package release Number Parameters Captured features studied neurite length, #, branching, density velocity of neurite growth or retraction varicosities in synapse formation neurite thickness

turning, retraction, extension, collapse

Criteria of cell selection/analysis Biased/unbiased Sholl Analysis linear / semi-log / log-log Are neurites touching? How was thresholding done

Y/N


Minimum Information About a Spinal Cord Injury experiment TAB 11 Behavior Frequency of testing Devices Time of day Observers blinded to treatments? Analgesics Hydration Antibiotics Motor Basso, Beattie, Bresnahan Locomotor Rating Scale (BBB) for rats BBB subscore Basso Mouse Scale BMS subscore Raters Paired Discussion Interrater correlation Training certification Gait Analysis Print area method Stride length method Step distribution method Base of support method Tread Scan Gait Analysis manufacture Gait Analysis model Gait Analysis Software and version # Sensory Cognitive Autonomic

Y/N Y/N Y/N Y/N

kind kind kind

Y/N Y/N Y/N Y/N Y/N Y/N Y/N Y/N Y/N Y/N Y/N Y/N

free text free text free text

When

dose amount dose

frequency when releatve to testing frequency when releatve to testing frequency when releatve to testing


Minimum Information About a Spinal Cord Injury experiment TAB 12 Experimental Design, Data Analysis, Statistics How and when were investigators blinded to experimental treatments

Example free text

Number of independent experiments for a study? What does independent mean?

free text

different animals, days, wells, cells, slices?

What is a technical replicate? Describe the prospective analysis plan Was primary outcome measure set prior to start of study?

free text free text Y/N

different animals, days, wells, cells, slices?

Statistical tests: what tests were used

free text

Normalization methods

free text

Technical replicates

Positive and negative controls

free text

DMSO, other solvent, neutral gene, scrambled oligonucleotide, transfection regent,

Notes

Complete spinal cord injury: an indication for spinal cord stimulation?

Spinal cord injury rehabilitation.

Hypothermia for spinal cord injury.

Spinal cord injury rehabilitation.

Spinal cord injury pain.

Acute spinal-cord injury.

Walking Index for Spinal Cord Injury version II in acute spinal cord injury: reliability and reproducibility.

Spinal cord injury models: a review.

Adiposity and spinal cord injury.

Thrombosis in spinal cord injury.

Pregnancy following spinal cord injury.

Suicide following spinal cord injury.

Spinal cord injury and pregnancy.

Sphingolipids in spinal cord injury.

Pathophysiology of spinal cord injury.

Treatment of spinal-cord injury.

Cervical spinal cord injury without bony injury.

Sleeping with spinal cord injury.

Depression and spinal cord injury.

Epidemiology of spinal cord injury.

Spinal cord injury models: neurophysiology.

Information in the early stages after spinal cord injury.

Sexuality for women with spinal cord injury.

Methylprednisolone for acute spinal cord injury.