Methodical advances in reproducibility research : A proof of concept qualitative comparative analysis of reproducing animal data in humans

Background: While the term reproducibility crisis mainly reflects reproducibility of experiments between laboratories, reproducibility between species also remains problematic. We previously summarised the published reproducibility between animal and human studies; i.e. the translational success rates, which varied from 0% to 100%. Based on analyses of individual factors, we could not predict reproducibility. Several potential analyses can assess effect of combinations of predictors on an outcome. Regression analysis (RGA) is common, but not ideal to analyse multiple interactions and specific configurations (≈ combinations) of variables, which could be highly relevant to reproducibility. Qualitative comparative analysis (QCA) is based on set theory and Boolean algebra, and was successfully used in other fields. We reanalysed the data from our preceding review with QCA. Results: This QCA resulted in the following preliminary formula for successful translation: ∼Old*∼Intervention*∼Large*MultSpec*Quantitative Which means that within the analysed dataset, the combination of relative recency (∼ means not; >1999), analyses at event or study level (not at intervention level), n 85%). Other combinations of factors showed less consistent or negative results. An RGA on the same data did not identify any of the included variables as significant contributors. Conclusions: While these data were not collected with the QCA in mind, they illustrate that the approach is viable and relevant for this research field. The QCA seems a highly promising approach to furthering our knowledge on between-species reproducibility

Intracerebral adenosine during sleep deprivation : A meta-analysis and new experimental data

Funding Information: The systematic review was funded by The Netherlands Organisation for Health Research and Development (ZonMW; 114024101); R2N, Federal State of Lower Saxony; and the DFG (FOR2591, BL 953/11-1). The microdialysis experiment was funded by Netherlands Organization for Scientific Research (NWO; 051-04-010, to Eus van Some-ren). The HPLC adenosine measurements were funded by the University of Helsinki sleep team and a travel grant from the European Sleep Research Society. Publisher Copyright: © 2018 Ubiquity Press. All rights reserved.The neuroregulator adenosine is involved in sleep-wake control. Basal forebrain (BF) adenosine levels increase during sleep deprivation. Only a few studies have addressed the effect of sleep deprivation on extracellular adenosine concentrations in other brain regions. In this paper, we describe a microdialysis experiment as well as a meta-analysis of published data. The 64 h microdialysis experiment determined the extracellular adenosine and adenosine monophosphate (AMP) concentrations in the medial prefrontal cortex of rats before, during and after 12 h of sleep deprivation by forced locomotion. The meta-analysis comprised published sleep deprivation animal experiments measuring adenosine by means of microdialysis. In the animal experiment, the overall median adenosine concentration was 0.36 nM and ranged from 0.004 nM to 27 nM. No significant differences were observed between the five conditions: 12 h of washout, baseline light phase, baseline dark phase, 12 h of sleep deprivation and 12 h of subsequent recovery. The overall median AMP concentration was 0.10 nM and ranged from 0.001 nM to 7.56 nM. Median AMP concentration increased during sleep deprivation (T = 47; p = 0.047) but normalised during subsequent recovery. The meta-analysis indicates that BF dialysate adenosine concentrations increase with 74.7% (95% CI: 54.1-95.3%) over baseline during sleep deprivation. Cortex dialysate adenosine concentrations during sleep deprivation were so far only reported by 2 publications. The increase in adenosine during sleep deprivation might be specific to the BF. At this stage, the evidence for adenosine levels in other brain regions is based on single experiments and insufficient for generalised conclusions. Further experiments are currently still warranted.Peer reviewe

Glucocorticoids in relation to behavior, morphology, and physiology as proxy indicators for the assessment of animal welfare: A systematic mapping review

Translating theoretical concepts of animal welfare into quantitative assessment protocols is an ongoing challenge. Glucocorticoids (GCs) are frequently used as physiological measure in welfare assessment. The interpretation of levels of GCs and especially their relation to welfare, however, is not as straightforward, questioning the informative power of GCs. The aim of this systematic mapping review was therefore to provide an overview of the relevant literature to identify global patterns in studies using GCs as proxy for the assessment of welfare of vertebrate species. Following a systematic protocol and a-priory inclusion criteria, 509 studies with 517 experiments were selected for data extraction. The outcome of the experiments was categorized based on whether the intervention significantly affected levels of GCs, and whether these effects were accompanied by changes in behavior,morphology and physiology. Additional information, such as animal species, type of intervention, experimental set up and sample type used for GC determination was extracted, as well. Given the broad scope and large variation in included experiments,meta-analyses were not performed, but outcomes are presented to encourage further, in-depth analyses of the data set. The interventions did not consistently lead to changes in GCs with respect to the original authors hypothesis. Changes in GCs were not consistently paralleled by changes in additional assessment parameter on behavior, morphology and physiology. The minority of experiment quantified GCs in less invasive sample matrices compared to blood. Interventions showed a large variability, and species such as fish were underrepresented, especially in the assessment of behavior. The inconclusive effects on GCs and additional assessment parameter urges for further validation of techniques and welfare proxies. Several conceptual and technical challenges need to be met to create standardized and robust welfare assessment protocols and to determine the role of GCs herein

Glucocorticoids in relation to behavior, morphology, and physiology as proxy indicators for the assessment of animal welfare. A systematic mapping review

Translating theoretical concepts of animal welfare into quantitative assessment protocols is an ongoing challenge. Glucocorticoids (GCs) are frequently used as physiological measure in welfare assessment. The interpretation of levels of GCs and especially their relation to welfare, however, is not as straightforward, questioning the informative power of GCs. The aim of this systematic mapping review was therefore to provide an overview of the relevant literature to identify global patterns in studies using GCs as proxy for the assessment of welfare of vertebrate species. Following a systematic protocol and a-priory inclusion criteria, 509 studies with 517 experiments were selected for data extraction. The outcome of the experiments was categorized based on whether the intervention significantly affected levels of GCs, and whether these effects were accompanied by changes in behavior, morphology and physiology. Additional information, such as animal species, type of intervention, experimental set up and sample type used for GC determination was extracted, as well. Given the broad scope and large variation in included experiments, meta-analyses were not performed, but outcomes are presented to encourage further, in-depth analyses of the data set. The interventions did not consistently lead to changes in GCs with respect to the original authors hypothesis. Changes in GCs were not consistently paralleled by changes in additional assessment parameter on behavior, morphology and physiology. The minority of experiment quantified GCs in less invasive sample matrices compared to blood. Interventions showed a large variability, and species such as fish were underrepresented, especially in the assessment of behavior. The inconclusive effects on GCs and additional assessment parameter urges for further validation of techniques and welfare proxies. Several conceptual and technical challenges need to be met to create standardized and robust welfare assessment protocols and to determine the role of GCs herein

Risk-Based Decision Making: A Systematic Scoping Review of Animal Models and a Pilot Study on the Effects of Sleep Deprivation in Rats

Animals, including humans, frequently make decisions involving risk or uncertainty. Different strategies in these decisions can be advantageous depending the circumstances. Short sleep duration seems to be associated with more risky decisions in humans. Animal models for risk-based decision making can increase mechanistic understanding, but very little data is available concerning the effects of sleep. We combined primary- and meta-research to explore the relationship between sleep and risk-based decision making in animals. Our first objective was to create an overview of the available animal models for risky decision making. We performed a systematic scoping review. Our searches in Pubmed and Psychinfo retrieved 712 references, of which 235 were included. Animal models for risk-based decision making have been described for rodents, non-human primates, birds, pigs and honey-bees. We discuss task designs and model validity. Our second objective was to apply this knowledge and perform a pilot study on the effect of sleep deprivation. We trained and tested male Wistar rats on a probability discounting task; a “safe” lever always resulted in 1 reward, a “risky” lever resulted in 4 or no rewards. Rats adapted their preferences to variations in reward probabilities (p < 0.001), but 12 h of sleep deprivation during the light phase did not clearly alter risk preference (p = 0.21)

Intracerebral adenosine during sleep deprivation : A meta-analysis and new experimental data

Funding Information: The systematic review was funded by The Netherlands Organisation for Health Research and Development (ZonMW; 114024101); R2N, Federal State of Lower Saxony; and the DFG (FOR2591, BL 953/11-1). The microdialysis experiment was funded by Netherlands Organization for Scientific Research (NWO; 051-04-010, to Eus van Some-ren). The HPLC adenosine measurements were funded by the University of Helsinki sleep team and a travel grant from the European Sleep Research Society. Publisher Copyright: © 2018 Ubiquity Press. All rights reserved.The neuroregulator adenosine is involved in sleep-wake control. Basal forebrain (BF) adenosine levels increase during sleep deprivation. Only a few studies have addressed the effect of sleep deprivation on extracellular adenosine concentrations in other brain regions. In this paper, we describe a microdialysis experiment as well as a meta-analysis of published data. The 64 h microdialysis experiment determined the extracellular adenosine and adenosine monophosphate (AMP) concentrations in the medial prefrontal cortex of rats before, during and after 12 h of sleep deprivation by forced locomotion. The meta-analysis comprised published sleep deprivation animal experiments measuring adenosine by means of microdialysis. In the animal experiment, the overall median adenosine concentration was 0.36 nM and ranged from 0.004 nM to 27 nM. No significant differences were observed between the five conditions: 12 h of washout, baseline light phase, baseline dark phase, 12 h of sleep deprivation and 12 h of subsequent recovery. The overall median AMP concentration was 0.10 nM and ranged from 0.001 nM to 7.56 nM. Median AMP concentration increased during sleep deprivation (T = 47; p = 0.047) but normalised during subsequent recovery. The meta-analysis indicates that BF dialysate adenosine concentrations increase with 74.7% (95% CI: 54.1-95.3%) over baseline during sleep deprivation. Cortex dialysate adenosine concentrations during sleep deprivation were so far only reported by 2 publications. The increase in adenosine during sleep deprivation might be specific to the BF. At this stage, the evidence for adenosine levels in other brain regions is based on single experiments and insufficient for generalised conclusions. Further experiments are currently still warranted.Peer reviewe

Animal to human translation : A systematic scoping review of reported concordance rates

Background: Drug development is currently hampered by high attrition rates; many developed treatments fail during clinical testing. Part of the attrition may be due to low animal-to-human translational success rates; so-called "translational failure". As far as we know, no systematic overview of published translational success rates exists. Systematic scoping review: The following research question was examined: "What is the observed range of the animal-to-human translational success (and failure) rates within the currently available empirical evidence?". We searched PubMed and Embase on 16 October 2017. We included reviews and all other types of "umbrella"-studies of meta-data quantitatively comparing the translational results of studies including at least two species with one being human. We supplemented our database searches with additional strategies. All abstracts and full-text papers were screened by two independent reviewers. Our scoping review comprises 121 references, with various units of measurement: compound or intervention (k = 104), study/experiment (k = 10), and symptom or event (k = 7). Diagnostic statistics corresponded with binary and continuous definitions of successful translation. Binary definitions comprise percentages below twofold error, percentages accurately predicted, and predictive values. Quantitative definitions comprise correlation/regression (r2) and meta-analyses (percentage overlap of 95% confidence intervals). Translational success rates ranged from 0 to 100%. Conclusion: The wide range of translational success rates observed in our study might indicate that translational success is unpredictable; i.e. it might be unclear upfront if the results of primary animal studies will contribute to translational knowledge. However, the risk of bias of the included studies was high, and much of the included evidence is old, while newer models have become available. Therefore, the reliability of the cumulative evidence from current papers on this topic is insufficient. Further in-depth "umbrella"-studies of translational success rates are still warranted. These are needed to evaluate the probabilistic evidence for predictivity of animal studies for the human situation more reliably, and to determine which factors affect this process

Spatial reversal learning is robust to total sleep deprivation

Sleep deprivation affects cognitive functions that depend on the prefrontal cortex (PFC) such as cognitive flexibility, and the consolidation of newly learned information. The identification of cognitive processes that are either robustly sensitive or robustly insensitive to the same experimental sleep deprivation procedure, will allow us to better focus on the specific effects of sleep on cognition, and increase understanding of the mechanisms involved. In the present study we investigate whether sleep deprivation differentially affects the two separate cognitive processes of acquisition and consolidation of a spatial reversal task.After training on a spatial discrimination between two levers in a Skinner box, male Wistar rats were exposed to a reversal of the previously learned stimulus-response contingency. We first evaluated the effect of sleep deprivation on the acquisition of reversal learning. Performance on reversal learning after 12. h of sleep deprivation (n=12) was compared to performance after control conditions (n=12). The second experiment evaluated the effect of sleep deprivation on the consolidation of reversal learning; the first session of reversal learning was followed by 3. h of nap prevention (n=8) or undisturbed control conditions (n=8). The experiments had sufficient statistical power (0.90 and 0.81, respectively) to detect differences with medium effect sizes.Neither the acquisition, nor the consolidation, of reversal learning was affected by acute sleep deprivation. Together with previous findings, these results help to further delineate the role of sleep in cognitive processing

Risk-Based Decision Making: A Systematic Scoping Review of Animal Models and a Pilot Study on the Effects of Sleep Deprivation in Rats

Animals, including humans, frequently make decisions involving risk or uncertainty. Different strategies in these decisions can be advantageous depending the circumstances. Short sleep duration seems to be associated with more risky decisions in humans. Animal models for risk-based decision making can increase mechanistic understanding, but very little data is available concerning the effects of sleep. We combined primary- and meta-research to explore the relationship between sleep and risk-based decision making in animals. Our first objective was to create an overview of the available animal models for risky decision making. We performed a systematic scoping review. Our searches in Pubmed and Psychinfo retrieved 712 references, of which 235 were included. Animal models for risk-based decision making have been described for rodents, non-human primates, birds, pigs and honey-bees. We discuss task designs and model validity. Our second objective was to apply this knowledge and perform a pilot study on the effect of sleep deprivation. We trained and tested male Wistar rats on a probability discounting task; a “safe” lever always resulted in 1 reward, a “risky” lever resulted in 4 or no rewards. Rats adapted their preferences to variations in reward probabilities (p < 0.001), but 12 h of sleep deprivation during the light phase did not clearly alter risk preference (p = 0.21)

A systematic mapping review of the evolution of the rat Forced Swim Test: Protocols and outcome parameters

As depression is projected to become the leading mental disease burden globally by 2030, understanding the underlying pathology, as well as screening potential anti-depressants with a higher efficacy, faster onset of action, and/or fewer side-effects is essential. A commonly used test for screening novel antidepressants and studying depression-linked aspects in rodents is the Porsolt Forced Swim Test. The present systematic mappping review gives a comprehensive overview of the evolution and of the most prevalently used set-ups of this test in rats, including the choice of animals (strain, sex, and age), technical aspects of protocol and environment, as well as reported outcome measures. Additionally, we provide an accessible list of all existing publications, to support informed decision-making for procedural and technical aspects of the test, to thereby enhance reproducibility and comparability. This should further contribute to reducing the number of unnecessarily replicated experiments, and consequently, reduce the number of animals used in future