Pre-Clinical Common Data Elements for Traumatic Brain Injury Research: Progress and Use Cases

A practical guide to data management and sharing for biomedical laboratory researchers

Effective data management and sharing have become increasingly crucial in biomedical research; however, many laboratory researchers lack the necessary tools and knowledge to address this challenge. This article provides an introductory guide into research data management (RDM), and the importance of FAIR (Findable, Accessible, Interoperable, and Reusable) data-sharing principles for laboratory researchers produced by practicing scientists. We explore the advantages of implementing organized data management strategies and introduce key concepts such as data standards, data documentation, and the distinction between machine and human-readable data formats. Furthermore, we offer practical guidance for creating a data management plan and establishing efficient data workflows within the laboratory setting, suitable for labs of all sizes. This includes an examination of requirements analysis, the development of a data dictionary for routine data elements, the implementation of unique subject identifiers, and the formulation of standard operating procedures (SOPs) for seamless data flow. To aid researchers in implementing these practices, we present a simple organizational system as an illustrative example, which can be tailored to suit individual needs and research requirements. By presenting a user-friendly approach, this guide serves as an introduction to the field of RDM and offers practical tips to help researchers effortlessly meet the common data management and sharing mandates rapidly becoming prevalent in biomedical research.

Traumatic Brain Injury and Neuromodulation Techniques in Rehabilitation: A Scoping Review

BACKGROUND AND OBJECTIVES

Traumatic Brain Injury (TBI) is a condition in which an external force, usually a violent blow to the head, causes functional impairment in the brain. Neuromodulation techniques are thought to restore altered function in the brain, resulting in improved function and reduced symptoms. Brain stimulation can alter the firing of neurons, boost synaptic strength, alter neurotransmitters and excitotoxicity, and modify the connections in their neural networks. All these are potential effects on brain activity. Accordingly, this is a promising therapy for TBI. These techniques are flexible because they can target different brain areas and vary in frequency and amplitude. This review aims to investigate the recent literature about neuromodulation techniques used in the rehabilitation of TBI patients.

MATERIALS AND METHODS

The identification of studies was made possible by conducting online searches on PubMed, Web of Science, Cochrane, Embase, and Scopus databases. Studies published between 2013 and 2023 were selected. This review has been registered on OSF (JEP3S).

RESULTS

We have found that neuromodulation techniques can improve the rehabilitation process for TBI patients in several ways. Transcranial Magnetic Stimulation (TMS) can improve cognitive functions such as recall ability, neural substrates, and overall improved performance on neuropsychological tests. Repetitive TMS has the potential to increase neural connections in many TBI patients but not in all patients, such as those with chronic diffuse axonal damage.

CONCLUSIONS

This review has demonstrated that neuromodulation techniques are promising instruments in the rehabilitation field, including those affected by TBI. The efficacy of neuromodulation can have a significant impact on their lives and improve functional outcomes for TBI patients.

Prolonging the therapeutic window for valproic acid treatment in a swine model of traumatic brain injury and hemorrhagic shock

BACKGROUND

It has previously been shown that administration of valproic acid (VPA) can improve outcomes if given within an hour following traumatic brain injury (TBI). This short therapeutic window (TW) limits its use in real-life situations. Based upon its pharmacokinetic data, we hypothesized that TW can be extended to 3 hours if a second dose of VPA is given 8 hours after the initial dose.

METHOD

Yorkshire swine (40-45 kg; n = 10) were subjected to TBI (controlled cortical impact) and 40% blood volume hemorrhage. After 2 hours of shock, they were randomized to either (1) normal saline resuscitation (control) or (2) normal saline-VPA (150 mg/kg × two doses). First dose of VPA was started 3 hours after the TBI, with a second dose 8 hours after the first dose. Neurologic severity scores (range, 0-36) were assessed daily for 14 days, and brain lesion size was measured via magnetic resonance imaging on postinjury day 3.

RESULTS

Hemodynamic and laboratory parameters of shock were similar in both groups. Valproic acid-treated animals had significantly less neurologic impairment on days 2 (16.3 ± 2.0 vs. 7.3 ± 2.8) and 3 (10.9 ± 3.6 vs. 2.8 ± 1.1) postinjury and returned to baseline levels 54% faster. Magnetic resonance imaging showed no differences in brain lesion size on day 3. Pharmacokinetic data confirmed neuroprotective levels of VPA in the circulation.

CONCLUSION

This is the first study to demonstrate that VPA can be neuroprotective even when given 3 hours after TBI. This expanded TW has significant implications for the design of the clinical trial.

Increasing Rigor of Preclinical Research to Maximize Opportunities for Translation

The use of animal models in pre-clinical research has significantly broadened our understanding of the pathologies that underlie traumatic brain injury (TBI)-induced damage and deficits. However, despite numerous pre-clinical studies reporting the identification of promising neurotherapeutics, translation of these therapies to clinical application has so far eluded the TBI research field. A concerted effort to address this lack of translatability is long overdue. Given the inherent heterogeneity of TBI and the replication crisis that continues to plague biomedical research, this is a complex task that will require a multifaceted approach centered around rigor and reproducibility. Here, we discuss the role of three primary focus areas for better aligning pre-clinical research with clinical TBI management. These focus areas are (1) reporting and standardization of protocols, (2) replication of prior knowledge including the confirmation of expected pharmacodynamics, and (3) the broad application of open science through inter-center collaboration and data sharing. We further discuss current efforts that are establishing the core framework needed for successfully addressing the translatability crisis of TBI.

A map of evidence using transcranial direct current stimulation (tDCS) to improve cognition in adults with traumatic brain injury (TBI)

Introduction

Cognition impairments often occur after a traumatic brain injury and occur at higher rates in military members. Cognitive symptoms impair daily function, including balance and life quality, years after the TBI. Current treatments to regain cognitive function after TBI, including medications and cognitive rehabilitation, have shown limited effectiveness. Transcranial direct current stimulation (tDCS) is a low-cost, non-invasive brain stimulation intervention that improves cognitive function in healthy adults and people with neuropsychologic diagnoses beyond current interventions. Despite the available evidence of the effectiveness of tDCS in improving cognition generally, only two small TBI trials have been conducted based on the most recent systematic review of tDCS effectiveness for cognition following neurological impairment. We found no tDCS studies that addressed TBI-related balance impairments.

Methods

A scoping review using a peer-reviewed search of eight databases was completed in July 2022. Two assessors completed a multi-step review and completed data extraction on included studies using a priori items recommended in tDCS and TBI research guidelines.

Results

A total of 399 results were reviewed for inclusion and 12 met the criteria and had data extracted from them by two assessors using Google Forms. Consensus on combined data results included a third assessor when needed. No studies using tDCS for cognition-related balance were found.

Discussion

Guidelines and technology measures increase the identification of brain differences that alter tDCS effects on cognition. People with mild-severe and acute-chronic TBI tolerated and benefited from tDCS. TBI-related cognition is understudied, and systematic research that incorporates recommended data elements is needed to advance tDCS interventions to improve cognition after TBI weeks to years after injury.

A model of traumatic brain injury in rats is influenced by neuroprotection of diurnal variation which improves motor behavior and histopathology in white matter myelin

Traumatic brain injury (TBI) represents a significant public health concern and has been associated with high rates of morbidity and mortality. TBI generates two types of brain damage: primary and secondary. Secondary damage originates a series of pathophysiological processes, which include metabolic crisis, excitotoxicity, and neuroinflammation, which have deleterious consequences for neuronal function. However, neuroprotective mechanisms are also activated. The balance among these tissue responses, and its variations throughout the day determines the fate of the damage tissue. We have demonstrated less behavioral and morphological damage when a rat model of TBI was induced during the light hours of the day. Moreover, here we show that rats subjected to TBI in the dark lost less body weight than those subjected to TBI in the light, despite no change in food intake. Besides, the rats subjected to TBI in the dark had better performance in the beam walking test and presented less histological damage in the corpus callosum and the cingulum bundle, as shown by the Klüver-Barrera staining. Our results suggest that the time of day when the injury occurs is important. Thus, this data should be used to evaluate the pathophysiological processes of TBI events and develop better therapies.

A Systematic Review and Meta-Analysis on the Therapeutic Efficacy of Heparin and Low Molecular Weight Heparins in Animal Studies of Traumatic Brain Injury

The identification of effective pharmacotherapies for traumatic brain injury (TBI) remains a major challenge. Treatment with heparin and its derivatives is associated with neuroprotective effects after experimental TBI; however, the optimal dosage and method of administration, modes of action, and effects on hemorrhage remain unclear. Therefore, this review aimed to systematically evaluate, analyze, and summarize the available literature on the use of heparin and low molecular weight heparins (LMWHs) as treatment options for experimental TBI. We searched two online databases (PubMed and ISI Web of Science) to identify relevant studies. Data pertaining to TBI paradigm, animal subjects, drug administration, and all pathological and behavior outcomes were extracted. Eleven studies met our pre-specified inclusion criteria, and for outcomes with sufficient numbers, data from seven publications were analyzed in a weighted mean difference meta-analysis using a random-effects model. Study quality and risk of bias were also determined. Meta-analysis revealed that heparin and its derivatives decreased brain edema, leukocyte rolling, and vascular permeability, and improved neurological function. Further, treatment did not aggravate hemorrhage. These findings must be interpreted with caution, however, because they were determined from a limited number of studies with substantial heterogeneity. Also, overall study quality was low based on absences of data reporting, and potential publication bias was identified. Importantly, we found that there are insufficient data to evaluate the variables we had hoped to investigate. The beneficial effects of heparin and LMWHs, however, suggest that further pre-clinical studies are warranted.

Defining Experimental Variability in Actuator-Driven Closed Head Impact in Rats

Traumatic brain injury (TBI) is a world-wide health challenge that lacks tools for diagnosis and treatment. There is a need for translational preclinical models to effectively design clinical tools, however, the diversity of models is a barrier to reproducible studies. Actuator-driven closed head impact (AD-CHI) models have translational advantages in replicating the pathophysiological and behavioral outcomes resulting from impact TBI. The main advantages of AD-CHI protocols include versatility of impact parameters such as impact angle, velocity, depth, and dwell time with the ability to interchange tip types, leading to consistent outcomes without the need for craniectomy. Sources of experimental variability within AD-CHI rat models are identified within this review with the aim of supporting further characterization to improve translational value. Primary areas of variability may be attributed to lack of standardization of head stabilization methods, reporting of tip properties, and performance of acute neurological assessments. AD-CHI models were also found to be more prevalently used among pediatric and repeated TBI paradigms. As this model continues to grow in use, establishing the relationships between impact parameters and associated injury outcomes will reduce experimental variability between research groups and encourage meaningful discussions as the community moves towards common data elements.

Empowering Data Sharing and Analytics through the Open Data Commons for Traumatic Brain Injury Research

Traumatic brain injury (TBI) is a major public health problem. Despite considerable research deciphering injury pathophysiology, precision therapies remain elusive. Here, we present large-scale data sharing and machine intelligence approaches to leverage TBI complexity. The Open Data Commons for TBI (ODC-TBI) is a community-centered repository emphasizing Findable, Accessible, Interoperable, and Reusable data sharing and publication with persistent identifiers. Importantly, the ODC-TBI implements data sharing of individual subject data, enabling pooling for high-sample-size, feature-rich data sets for machine learning analytics. We demonstrate pooled ODC-TBI data analyses, starting with descriptive analytics of subject-level data from 11 previously published articles (N = 1250 subjects) representing six distinct pre-clinical TBI models. Second, we perform unsupervised machine learning on multi-cohort data to identify persistent inflammatory patterns across different studies, improving experimental sensitivity for pro- versus anti-inflammation effects. As funders and journals increasingly mandate open data practices, ODC-TBI will create new scientific opportunities for researchers and facilitate multi-data-set, multi-dimensional analytics toward effective translation.

Therapeutic potential of nociceptin/orphanin FQ peptide (NOP) receptor modulators for treatment of traumatic brain injury, traumatic stress, and their co-morbidities

The nociceptin/orphanin FQ (N/OFQ) peptide (NOP) receptor is a member of the opioid receptor superfamily with N/OFQ as its endogenous agonist. Wide expression of the NOP receptor and N/OFQ, both centrally and peripherally, and their ability to modulate several biological functions has led to development of NOP receptor modulators by pharmaceutical companies as therapeutics, based upon their efficacy in preclinical models of pain, anxiety, depression, Parkinson's disease, and substance abuse. Both posttraumatic stress disorder (PTSD) and traumatic brain injury (TBI) are debilitating conditions that significantly affect the quality of life of millions of people around the world. PTSD is often a consequence of TBI, and, especially for those deployed to, working and/or living in a war zone or are first responders, they are comorbid. PTSD and TBI share common symptoms, and negatively influence outcomes as comorbidities of the other. Unfortunately, a lack of effective therapies or therapeutic agents limits the long term quality of life for either TBI or PTSD patients. Ours, and other groups, demonstrated that PTSD and TBI preclinical models elicit changes in the N/OFQ-NOP receptor system, and that administration of NOP receptor ligands alleviated some of the neurobiological and behavioral changes induced by brain injury and/or traumatic stress exposure. Here we review the past and most recent progress on understanding the role of the N/OFQ-NOP receptor system in PTSD and TBI neurological and behavioral sequelae. There is still more to understand about this neuropeptide system in both PTSD and TBI, but current findings warrant further examination of the potential utility of NOP modulators as therapeutics for these disorders and their co-morbidities. We advocate the development of standards for common data elements (CDE) reporting for preclinical PTSD studies, similar to current preclinical TBI CDEs. That would provide for more standardized data collection and reporting to improve reproducibility, interpretation and data sharing across studies.

Differential association of baseline body weight and body-weight loss with neurological deficits, histology, and death after repetitive closed head traumatic brain injury

Clinical observations indicate that body weight (BW) extremes are associated with worse outcome after traumatic brain injury (TBI); yet, it is uncertain whether the baseline BW (bBW) may affect outcome after mouse TBI. We retrospectively analyzed 129 similarly aged (9-12 weeks) male C57BL6/J mice that were subjected to repetitive closed head TBI (rTBI) using an established weight drop paradigm as well as 55 sham injured mice. We sought to determine whether the bBW as well as the post-TBI weight relative to baseline (%BW) were associated with a variety of post-rTBI outcomes, including acute model complications (skull fractures and macroscopic hemorrhage), impact seizures, return of the righting reflex (RR), the neurological severity score (NSS), post-rTBI BW-change, and 28-day mortality. In a subset of rTBI mice, we also assessed for potential associations between the bBW and %BW and performance in the novel object recognition (NOR) task and various histological outcomes at 28 days. We found no association between the bBW with acute model complications, impact seizure burden, RR, NSS, and NOR performance at 28 days, as well as cerebral microbleed burden, presence of hyperphosphorylated tau, and TDP-43 pathology after rTBI. However, a higher bBW was associated with a longer time to first impact seizure, a greater microglial activation, astrocytosis, and neuronal loss in the injured cerebral cortex at 28 days. A greater %BW-loss was associated with a shorter impact seizure-free survival, longer time to return of the righting reflex, greater neurological deficit severity as assessed by the NSS and NOR, and worse mortality. On multiple linear regression there was no independent association of the %BW-loss with neuronal loss and neuroinflammation after adjustment for the bBW. These observations indicate that the bBW and %BW-loss may be important biological variables in certain experimental mouse TBI investigations, depending on the outcome measures of interest.

Feeding the machine: Challenges to reproducible predictive modeling in resting-state connectomics

In this critical review, we examine the application of predictive models, for example, classifiers, trained using machine learning (ML) to assist in interpretation of functional neuroimaging data. Our primary goal is to summarize how ML is being applied and critically assess common practices. Our review covers 250 studies published using ML and resting-state functional MRI (fMRI) to infer various dimensions of the human functional connectome. Results for holdout ("lockbox") performance was, on average, ∼13% less accurate than performance measured through cross-validation alone, highlighting the importance of lockbox data, which was included in only 16% of the studies. There was also a concerning lack of transparency across the key steps in training and evaluating predictive models. The summary of this literature underscores the importance of the use of a lockbox and highlights several methodological pitfalls that can be addressed by the imaging community. We argue that, ideally, studies are motivated both by the reproducibility and generalizability of findings as well as the potential clinical significance of the insights. We offer recommendations for principled integration of machine learning into the clinical neurosciences with the goal of advancing imaging biomarkers of brain disorders, understanding causative determinants for health risks, and parsing heterogeneous patient outcomes.

Measuring Anxiety-Like Behaviors in Rodent Models of Traumatic Brain Injury

Anxiety is a common complaint following acquired traumatic brain injury (TBI). However, the measurement of dysfunctional anxiety behavioral states following experimental TBI in rodents is complex. Some studies report increased anxiety after TBI, whereas others find a decreased anxiety-like state, often described as increased risk-taking behavior or impulsivity. These inconsistencies may reflect a lack of standardization of experimental injury models or of behavioral testing techniques. Here, we review the most commonly employed unconditioned tests of anxiety and discuss them in a context of experimental TBI. Special attention is given to the effects of repeated testing, and consideration of potential sensory and motor confounds in injured rodents. The use of multiple tests and alternative data analysis methods are discussed, as well as the potential for the application of common data elements (CDEs) as a means of providing a format for documentation of experimental details and procedures of each published research report. CDEs may improve the rigor, reproducibility, as well as endpoint for better relating findings with clinical TBI phenotypes and the final goal of translation. While this may not resolve all incongruities in findings across laboratories, it is seen as a way forward for standardized and universal data collection for improvement of data quality and sharing, and advance therapies for neuropsychiatric symptoms that often present for decades following TBI.

PEERS - An Open Science "Platform for the Exchange of Experimental Research Standards" in Biomedicine

Laboratory workflows and preclinical models have become increasingly diverse and complex. Confronted with the dilemma of a multitude of information with ambiguous relevance for their specific experiments, scientists run the risk of overlooking critical factors that can influence the planning, conduct and results of studies and that should have been considered a priori. To address this problem, we developed "PEERS" (Platform for the Exchange of Experimental Research Standards), an open-access online platform that is built to aid scientists in determining which experimental factors and variables are most likely to affect the outcome of a specific test, model or assay and therefore ought to be considered during the design, execution and reporting stages. The PEERS database is categorized into in vivo and in vitro experiments and provides lists of factors derived from scientific literature that have been deemed critical for experimentation. The platform is based on a structured and transparent system for rating the strength of evidence related to each identified factor and its relevance for a specific method/model. In this context, the rating procedure will not solely be limited to the PEERS working group but will also allow for a community-based grading of evidence. We here describe a working prototype using the Open Field paradigm in rodents and present the selection of factors specific to each experimental setup and the rating system. PEERS not only offers users the possibility to search for information to facilitate experimental rigor, but also draws on the engagement of the scientific community to actively expand the information contained within the platform. Collectively, by helping scientists search for specific factors relevant to their experiments, and to share experimental knowledge in a standardized manner, PEERS will serve as a collaborative exchange and analysis tool to enhance data validity and robustness as well as the reproducibility of preclinical research. PEERS offers a vetted, independent tool by which to judge the quality of information available on a certain test or model, identifies knowledge gaps and provides guidance on the key methodological considerations that should be prioritized to ensure that preclinical research is conducted to the highest standards and best practice.

Roadmap for Advancing Pre-Clinical Science in Traumatic Brain Injury

Pre-clinical models of disease have long played important roles in the advancement of new treatments. However, in traumatic brain injury (TBI), despite the availability of numerous model systems, translation from bench to bedside remains elusive. Integrating clinical relevance into pre-clinical model development is a critical step toward advancing therapies for TBI patients across the spectrum of injury severity. Pre-clinical models include in vivo and ex vivo animal work-both small and large-and in vitro modeling. The wide range of pre-clinical models reflect substantial attempts to replicate multiple aspects of TBI sequelae in humans. Although these models reveal multiple putative mechanisms underlying TBI pathophysiology, failures to translate these findings into successful clinical trials call into question the clinical relevance and applicability of the models. Here, we address the promises and pitfalls of pre-clinical models with the goal of evolving frameworks that will advance translational TBI research across models, injury types, and the heterogenous etiology of pathology.