The Road to Reproducibility in Animal Research

Still to ARRIVE at adequate reporting of orthodontic studies involving animal models

BACKGROUND

The ARRIVE 2.0 guidelines were introduced to improve the reporting of animal studies. The aim of this study was to assess the reporting adherence of orthodontic speciality animal studies in relation to ARRIVE 2.0 guidelines. Associations between the reporting and study characteristics were explored.

MATERIALS AND METHOD

An electronic database search was undertaken using Medline via PubMed (www.pubmed.ncbi.nlm.nih.gov) to identify studies meeting the eligibility criteria published between 1 January 2018 and 31 December 2023. Data extraction was performed in duplicate and independently. Descriptive statistics and frequency distributions for the responses to each checklist item were calculated. Mean values for adequate reporting per ARRIVE item were calculated. A sum score was calculated by adding the responses (0 = not reported, 1 = inadequate reporting, 2 = adequate reporting) per item and sub-questions. On an exploratory basis, univariable linear regression between summary score and study characteristics (year of publication, continent of authorship, type of centre, and number of authors) was performed.

RESULTS

Three hundred and eighty-four studies were analysed. Variability in the adequate reporting of the ARRIVE 2.0 guideline items was evident. In particular, in 32% of studies, there was a lack of reporting of the priori sample size calculation. Overall, the mean reporting score for the sample was 57.9 (SD 6.7 and range 34-74). There were no associations between score and study characteristics except for a weak association for year of publication with a small improvement over time (each additional year).

CONCLUSIONS

The reporting of animal studies relevant to the speciality of orthodontics is sub-optimal in relation to the ARRIVE 2.0 guidelines. There was a tendency for the non-reporting of items pertaining to study sample size, eligibility, methods to reduce bias and interpretation/scientific implications. Greater awareness and reporting adherence to the ARRIVE 2.0 guidelines are required to reduce research waste involving animal models.

A mapping review of refinements to laboratory rat housing and husbandry

Refining the housing and husbandry of laboratory rats is an important goal, both for ethical reasons and to allow better quality research. We conducted a mapping review of 1,017 studies investigating potential refinements of housing and husbandry of the laboratory rat to assess what refinements have, and have not, been studied, and to briefly assess whether there is evidence to support any impact on rat welfare. Among the many refinements studied, the majority involve changes to the cage, but some also involve alterations to the wider environment. The effects of these refinements were assessed using a range of readouts, many of which are difficult to interpret from a welfare perspective. Preference studies, which are easier to interpret, provide evidence that rats prefer complex environments, including shelters and multiple objects, which offer different areas/resources allowing the rat to engage in diverse behaviors. The reporting of methodology in papers was often poor, indicating that studies were potentially subject to biases. Given that many refinements co-occurred, it was often difficult to tease apart which ones were most beneficial for rat welfare. Effects of refinements were also moderated by a number of factors including age, sex, strain and photoperiod. Altogether our findings show that a one-size-fits-all approach to refinements is not appropriate, because different refinements will impact different rats in different ways. Our review has also produced a database of >1,000 articles that can be used for further and more detailed analyses. Our findings have also highlighted areas where future research is likely to be valuable, including refinements to rat transport, handling and the use of training.

Touchscreen cognitive testing: Cross-species translation and co-clinical trials in neurodegenerative and neuropsychiatric disease

Translating results from pre-clinical animal studies to successful human clinical trials in neurodegenerative and neuropsychiatric disease presents a significant challenge. While this issue is clearly multifaceted, the lack of reproducibility and poor translational validity of many paradigms used to assess cognition in animal models are central contributors to this challenge. Computer-automated cognitive test batteries have the potential to substantially improve translation between pre-clinical studies and clinical trials by increasing both reproducibility and translational validity. Given the structured nature of data output, computer-automated tests also lend themselves to increased data sharing and other open science good practices. Over the past two decades, computer automated, touchscreen-based cognitive testing methods have been developed for non-human primate and rodent models. These automated methods lend themselves to increased standardization, hence reproducibility, and have become increasingly important for the elucidation of the neurobiological basis of cognition in animal models. More recently, there have been increased efforts to use these methods to enhance translational validity by developing task batteries that are nearly identical across different species via forward (i.e., translating animal tasks to humans) and reverse (i.e., translating human tasks to animals) translation. An additional benefit of the touchscreen approach is that a cross-species cognitive test battery makes it possible to implement co-clinical trials-an approach developed initially in cancer research-for novel treatments for neurodegenerative disorders. Co-clinical trials bring together pre-clinical and early clinical studies, which facilitates testing of novel treatments in mouse models with underlying genetic or other changes, and can help to stratify patients on the basis of genetic, molecular, or cognitive criteria. This approach can help to determine which patients should be enrolled in specific clinical trials and can facilitate repositioning and/or repurposing of previously approved drugs. This has the potential to mitigate the resources required to study treatment responses in large numbers of human patients.

Bioethical, Reproducibility, and Translational Challenges of Animal Models

There is no prescribed stage or standardized point at which an animal model protocol is reviewed for reproducibility and translatability. The method of review for a reproducible and translatable study is not consistently documented in peer literature, and this is a major challenge for those working with animal models of human diseases. If the study is ill designed, it is impossible to perform an accurate harm/benefit analysis. In addition, there may be an ethical challenge if the work is not reproducible and translatable. Animal welfare regulations and other documents of control clearly state the role of the Institutional Animal Care and Use Committees are to look at science justification within the context of animal welfare. This article, concentrating on models not governed by regulations, outlines issues and offers recommendations for refining animal model review with a goal to improve study reproducibility and translatability.

Effect of chronic unpredictable mild stress on the expression profile of serotonin receptors in rats and mice: a meta-analysis

Chronic-stress-induced depression is recognized as a widespread public health concern. Selective serotonin reuptake inhibitors (SSRIs) have been the most common treatment for this illness. However, the role of 5-hydroxytryptamine (5-HT) receptor subtypes in stress-induced depression remains unclear. Evidence from Animal studies has reported a variety of results regarding the effects of chronic unpredictable mild stress (CUMS) on serotonin signaling pathways and 5-HT receptor subtypes. This divergence may rely on differences in protocols, methods, and studied pathways. Thus, the aim of this systematic review was to weigh the currently available findings regarding serotonin receptor changes in animal models of CUMS. Overall, our meta-analysis results showed the association of altered expression of 5-HT_1A receptors in the frontal cortex and 5-HT_2A receptors both in the whole cortex and the hypothalamus of rats following CUMS. Moreover, by using a qualitative-structured analysis and the application of risk-of-bias tools, we identified possible sources of data variation between the studied literature, which should be taken into account in future animal studies of chronic-stress induced depression.

Common methodological issues and suggested solutions in bone research

Bone research is a dynamic area of scientific investigation that usually encompasses multidisciplines. Virtually all basic cellular research, clinical research and epidemiologic research rely on statistical concepts and methodology for inference. This paper discusses common issues and suggested solutions concerning the application of statistical thinking in bone research, particularly in clinical and epidemiological investigations. The issues are sample size estimation, biases and confounders, analysis of longitudinal data, categorization of continuous data, selection of significant variables, over-fitting, P-values, false positive finding, confidence interval, and Bayesian inference. It is hoped that by adopting the suggested measures the scientific quality of bone research can improve.

Inadequate awareness of adherence to ARRIVE guidelines, regarding reporting quality of hernia models repaired with meshes: a systematic review

PURPOSE

Research papers involving animal studies often display poor reporting standards, leading to lower study reproducibility. We aim to determine the difference in reporting animal studies regarding abdominal wall hernia repair with mesh placement, before and after the publication of ARRIVE-2010 (Animal Research: Reporting of In Vivo Experiments) guidelines. Furthermore, we aim to present the most up-to-date reporting quality using the updated ARRIVE-2020 as criteria.

METHODS

All animal studies concerning hernia repair with meshes were systematically searched. Articles published in the 5 years leading up to the ARRIVE-2010 (pre-ARRIVE) and articles within the last 5 years until the updated ARRIVE 2.0 (post-ARRIVE) were compared for overall species and specific species separately. Articles published last year were evaluated for presenting fully reported (sub)items.

RESULTS

The number of fully reported (sub)items per article was on average significantly higher for pre-ARRIVE than post-ARRIVE for overall species (mean (SD) = 14.0 (2.8) vs. 12.6 (2.5), P < 0.001). The same applies to rabbit (mean (SD) = 14.8 (2.6) vs. 12.6 (2.6), P = 0.001) and pig studies (mean (SD) = 14.5 (2.7) vs. 11.6 (2.6), P = 0.004), with no significance in rat studies (mean (SD) = 13.6 (2.9) vs. 12.9 (2.3), P = 0.076). Significance was found in several (sub)items between pre-ARRIVE and post-ARRIVE (n = 7, 3, 8, and 3 for overall species, rat, rabbit, and pig studies, respectively).

CONCLUSION

General reporting quality of animal experiments has been improved markedly by ARRIVE guidelines. However, more improvements are required considering the arrival of ARRIVE 2.0 guidelines.

Validation of alternative behavioral observation methods in young broiler chickens

Continuous sampling provides the most complete data set for behavioral research; however, it often requires a prohibitive investment of time and labor. The objectives of this study were to validate behavioral observation methods of young broiler chickens using 1) 7 scan sampling intervals (0.5, 1, 3, 5, 10, 15, and 30 min) and 2) an automated tracking software program (EthoVision XT 14) compared to continuous behavioral observation, considered the gold standard for behavior observation. Ten 19-day-old Ross 708 broiler cockerels were included in this study. All behavior was video recorded over an 8-h period, and data were collected using a continuous sampling methodology. The same video files were utilized for analysis for scan sampling and automated tracking software analysis. For both analyses, the following criteria were used to identify which method accurately reflected the true duration and frequency for each behavior, as determined by continuous observation: R² ≥ 0.9, slope was not different from 1 (P > 0.05), and intercept was not different from 0 (P > 0.05). Active, eating, drinking, and maintenance behaviors were accurately estimated with 0.5-min scan sample intervals. Active, inactive, eating, and maintenance behaviors were accurately estimated with 1-min scan sample intervals. Inactive behavior was accurately estimated with 5-min scan sample intervals. The remainder of sampling intervals examined did not provide accurate estimates, and no scan sampling interval accurately estimated the number of behavior bouts. The automated tracking software was able to accurately detect true duration of inactive behavior but was unable to accurately detect activity. The results of this study suggest that high-frequency behaviors can be accurately observed with instantaneous scan sampling up to 1-min intervals. Automated tracking software can accurately identify inactivity in young broiler chickens, but further behavior identification will require refinement.

Scoping review on interventions to improve adherence to reporting guidelines in health research

OBJECTIVES

The goal of this study is to identify, analyse and classify interventions to improve adherence to reporting guidelines in order to obtain a wide picture of how the problem of enhancing the completeness of reporting of biomedical literature has been tackled so far.

DESIGN

Scoping review.

SEARCH STRATEGY

We searched the MEDLINE, EMBASE and Cochrane Library databases and conducted a grey literature search for (1) studies evaluating interventions to improve adherence to reporting guidelines in health research and (2) other types of references describing interventions that have been performed or suggested but never evaluated. The characteristics and effect of the evaluated interventions were analysed. Moreover, we explored the rationale of the interventions identified and determined the existing gaps in research on the evaluation of interventions to improve adherence to reporting guidelines.

RESULTS

109 references containing 31 interventions (11 evaluated) were included. These were grouped into five categories: (1) training on the use of reporting guidelines, (2) improving understanding, (3) encouraging adherence, (4) checking adherence and providing feedback, and (5) involvement of experts. Additionally, we identified lack of evaluated interventions (1) on training on the use of reporting guidelines and improving their understanding, (2) at early stages of research and (3) after the final acceptance of the manuscript.

CONCLUSIONS

This scoping review identified a wide range of strategies to improve adherence to reporting guidelines that can be taken by different stakeholders. Additional research is needed to assess the effectiveness of many of these interventions.

The importance of selection and reporting of the sex of experimental animals

Biased use of males and females in animal studies or omitting specific details of the sex of animals used in publications limits reproducibility, hampers the pace and likelihood of new discoveries and invites adverse events in ensuing clinical research. Hence unbiased use of males and females in animal studies and specific reporting of animal details are increasingly required by funding bodies and scientific journals worldwide. An analysis to determine how males and females are used in animal studies involving the Commonwealth Scientific and Industrial Research Organisation (CSIRO) was undertaken as part of a process to review and further support best practice. In the study 178 publications that contain animal studies and include CSIRO researchers published between January 2014 and December 2016 were analysed for the sex of animals used. The overall sex distribution was males only 26.4% (47/178), females only 15.7% (28/178), males and females 18.0% (32/178) and sex of animals unspecified 39.9% (71/178). Reasons for this distribution include species biology, farming practices and commercial relevance. Although including sex as an experimental variable provides the most information, using both sexes in an animal study requires careful consideration and planning. Furthermore, there are valid biological and experimental reasons why sex distribution in a study may not be balanced. Biological reasons include cases where the severity of disease in a given model differs between males and females, superior husbandry or production traits in one sex and hermaphroditic species that change sex with age. Examples where experiments can only be undertaken in one sex of animal include animal models of female breast cancer, female reproductive traits, male fertility studies and post-castration welfare outcomes. Where there is no biological or experimental reason for using a single sex of animal, future studies should obtain an estimate of sex effect either from the literature or with a pilot study, and experiments should be planned and reported accordingly.

Dietary Pyrophosphate Modulates Calcification in a Mouse Model of Pseudoxanthoma Elasticum: Implication for Treatment of Patients

Pseudoxanthoma elasticum is a heritable disease caused by ABCC6 deficiency. Patients develop ectopic calcification in skin, eyes, and vascular tissues. ABCC6, primarily found in liver and kidneys, mediates the cellular efflux of ATP, which is rapidly converted into inorganic pyrophosphate (PPi), a potent inhibitor of calcification. Pseudoxanthoma elasticum patients and Abcc6^-/- mice display reduced PPi levels in plasma and peripheral tissues. Pseudoxanthoma elasticum is currently incurable, although some palliative treatments exist. In recent years, we have successfully developed therapeutic methodologies to compensate the PPi deficit in animal models and humans. Here, we inadvertently discovered that modulating dietary PPi can also be an effective approach to reducing calcification in Abcc6^-/- mice. Our findings were prompted by a change in institutional rodent diet. The new chow was enriched in PPi, which increased plasma PPi, and significantly reduced mineralization in Abcc6^-/- mice. We also found that dietary PPi is readily absorbed in humans. Our results suggest that the consumption of food naturally or artificially enriched in PPi represents a possible intervention to mitigate calcification progression in pseudoxanthoma elasticum, that dietary preferences of patients may explain pseudoxanthoma elasticum heterogeneous manifestations, and that animal chow has the potential to influence data reproducibility.

The price of progress: Funding and financing Alzheimer's disease drug development

INTRODUCTION

Advancing research and treatment for Alzheimer's disease (AD) and the search for effective treatments depend on a complex financial ecosystem involving federal, state, industry, advocacy, venture capital, and philanthropy funding approaches.

METHODS

We conducted an expert review of the literature pertaining to funding and financing of translational research and drug development for AD.

RESULTS

The federal government is the largest public funder of research in AD. The National Institute on Aging, National Institute of Mental Health, National Institute of General Medical Sciences, and National Center for Advancing Translational Science all fund aspects of research in AD drug development. Non-National Institutes of Health federal funding comes from the National Science Foundation, Veterans Administration, Food and Drug Administration, and the Center for Medicare and Medicaid Services. Academic Medical Centers host much of the federally funded basic science research and are increasingly involved in drug development. Funding of the "Valley of Death" involves philanthropy and federal funding through small business programs and private equity from seed capital, angel investors, and venture capital companies. Advocacy groups fund both basic science and clinical trials. The Alzheimer Association is the advocacy organization with the largest research support portfolio relevant to AD drug development. Pharmaceutical companies are the largest supporters of biomedical research worldwide; companies are most interested in late stage de-risked drugs. Drugs progressing into phase II and III are candidates for pharmaceutical industry support through licensing, mergers and acquisitions, and co-development collaborations.

DISCUSSION

Together, the funding and financing entities involved in supporting AD drug development comprise a complex, interactive, dynamic financial ecosystem. Funding source interaction is largely unstructured and available funding is insufficient to meet all demands for new therapies. Novel approaches to funding such as mega-funds have been proposed and more integration of component parts would assist in accelerating drug development.

Impaired reproduction after exposure to ADHD drugs: Systematic review of animal studies

BACKGROUND:

Few studies have reported on long-term harms caused by ADHD drugs but they are known to impair growth.

OBJECTIVE:

To assess whether ADHD drugs impair reproduction in mammals.

METHODS:

Systematic review of reproduction in studies of animals treated with ADHD drugs.

DATA SOURCES:

PubMed, Biosis and EMBASE.

RESULTS:

We included 17 studies. The studies were generally of poor quality or poorly reported. Two studies reported the use of one of three advised randomisation methods. Fifteen studies used placebo which suggested blinding. On clonidine, the ability to produce offspring was reduced for male rats, which approached two females each. In one study, 10 treated rats produced no offspring while all four controls did. In another study, 10 treated rats impregnated nine females while 10 controls impregnated 16. On methylphenidate, vaginal opening was delayed in two studies (in one, the mean difference was 4.0 days, 95% CI 2.5 to 5.6, and number of estrous cycles was halved; in the other, the minimum delay was 6 days), while in two other studies no difference occurred. Generally, the impairments improved after a drug-free period and were less pronounced when treatment started later in life.

CONCLUSION:

ADHD drugs impair the reproduction in animals.

Vibration in mice: A review of comparative effects and use in translational research

Sound pressure waves surround individuals in everyday life and are perceived by animals and humans primarily through sound or vibration. When sound pressure waves traverse through a solid medium, vibration will result. Vibration has long been considered an unwanted variable in animal research and may confound scientific endeavors using animals. Understanding the characteristics of vibration is required to determine whether effects in animals are likely to be therapeutic or result in adverse biological effects. The eighth edition of the "Guide for the Care and Use of Laboratory Animals" highlights the importance of considering vibration and its effects on animals in the research setting, but knowledge of the level of vibration for eliciting these effects was unknown. The literature provides information regarding therapeutic use of vibration in humans, but the range of conditions to be of therapeutic benefit is varied and without clarity. Understanding the characteristics of vibration (eg, frequency and magnitude) necessary to cause various effects will ultimately assist in the evaluation of this environmental factor and its role on a number of potential therapeutic regimens for use in humans. This paper will review the principles of vibration, sources within a research setting, comparative physiological effects in various species, and the relative potential use of vibration in the mouse as a translational research model.

3S - Systematic, systemic, and systems biology and toxicology

A biological system is more than the sum of its parts - it accomplishes many functions via synergy. Deconstructing the system down to the molecular mechanism level necessitates the complement of reconstructing functions on all levels, i.e., in our conceptualization of biology and its perturbations, our experimental models and computer modelling. Toxicology contains the somewhat arbitrary subclass "systemic toxicities"; however, there is no relevant toxic insult or general disease that is not systemic. At least inflammation and repair are involved that require coordinated signaling mechanisms across the organism. However, the more body components involved, the greater the challenge to reca-pitulate such toxicities using non-animal models. Here, the shortcomings of current systemic testing and the development of alternative approaches are summarized. We argue that we need a systematic approach to integrating existing knowledge as exemplified by systematic reviews and other evidence-based approaches. Such knowledge can guide us in modelling these systems using bioengineering and virtual computer models, i.e., via systems biology or systems toxicology approaches. Experimental multi-organ-on-chip and microphysiological systems (MPS) provide a more physiological view of the organism, facilitating more comprehensive coverage of systemic toxicities, i.e., the perturbation on organism level, without using substitute organisms (animals). The next challenge is to establish disease models, i.e., micropathophysiological systems (MPPS), to expand their utility to encompass biomedicine. Combining computational and experimental systems approaches and the chal-lenges of validating them are discussed. The suggested 3S approach promises to leverage 21st century technology and systematic thinking to achieve a paradigm change in studying systemic effects.

Impact of Stroke Therapy Academic Industry Roundtable (STAIR) Guidelines on Peri-Anesthesia Care for Rat Models of Stroke: A Meta-Analysis Comparing the Years 2005 and 2015

Numerous studies using rats in stroke models have failed to translate into successful clinical trials in humans. The Stroke Therapy Academic Industry Roundtable (STAIR) has produced guidelines on the rodent stroke model for preclinical trials in order to promote the successful translation of animal to human studies. These guidelines also underline the importance of anaesthetic and monitoring techniques. The aim of this literature review is to document whether anaesthesia protocols (i.e., choice of agents, mode of ventilation, physiological support and monitoring) have been amended since the publication of the STAIR guidelines in 2009. A number of articles describing the use of a stroke model in adult rats from the years 2005 and 2015 were randomly selected from the PubMed database and analysed for the following parameters: country where the study was performed, strain of rats used, technique of stroke induction, anaesthetic agent for induction and maintenance, mode of intubation and ventilation, monitoring techniques, control of body temperature, vascular accesses, and administration of intravenous fluids and analgesics. For each parameter (stroke, induction, maintenance, monitoring), exact chi-square tests were used to determine whether or not proportions were significantly different across year and p values were corrected for multiple comparisons. An exact p-test was used for each parameter to compare the frequency distribution of each value followed by a Bonferroni test. The level of significant set at < 0.05. Results show that there were very few differences in the anaesthetic and monitoring techniques used between 2005 and 2015. In 2015, significantly more studies were performed in China and significantly fewer studies used isoflurane and nitrous oxide. The most striking finding is that the vast majority of all the studies from both 2005 and 2015 did not report the use of ventilation; measurement of blood gases, end-tidal carbon dioxide concentration, or blood pressure; or administration of intravenous fluids or analgesics. The review of articles published in 2015 showed that the STAIR guidelines appear to have had no effect on the anaesthetic and monitoring techniques in rats undergoing experimental stroke induction, despite the publication of said guidelines in 2009.

Fus1 KO Mouse As a Model of Oxidative Stress-Mediated Sporadic Alzheimer's Disease: Circadian Disruption and Long-Term Spatial and Olfactory Memory Impairments

Insufficient advances in the development of effective therapeutic treatments of sporadic Alzheimer's Disease (sAD) to date are largely due to the lack of sAD-relevant animal models. While the vast majority of models do recapitulate AD's hallmarks of plaques and tangles by virtue of tau and/or beta amyloid overexpression, these models do not reflect the fact that in sAD (unlike familial AD) these genes are not risk factors per se and that other mechanisms like oxidative stress, metabolic dysregulation and inflammation play key roles in AD etiology. Here we characterize and propose the Fus1 KO mice that lack a mitochondrial protein Fus1/Tusc2 as a new sAD model. To establish sAD relevance, we assessed sAD related deficits in Fus1 KO and WT adult mice of 4-5 months old, the equivalent human age when the earliest cognitive and olfactory sAD symptoms arise. Fus1 KO mice showed oxidative stress (increased levels of ROS, decreased levels of PRDX1), disruption of metabolic homeostasis (decreased levels of ACC2, increased phosphorylation of AMPK), autophagy (decreased levels of LC3-II), PKC (decreased levels of RACK1) and calcium signaling (decreased levels of Calb2) in the olfactory bulb and/or hippocampus. Mice were behaviorally tested using objective and accurate video tracking (Noldus), in which Fus1 KO mice showed clear deficits in olfactory memory (decreased habituation/cross-habituation in the short and long term), olfactory guided navigation memory (inability to reduce their latency to find the hidden cookie), spatial memory (learning impairments on finding the platform in the Morris water maze) and showed more sleep time during the diurnal cycle. Fus1 KO mice did not show clear deficits in olfactory perception (cross-habituation), association memory (passive avoidance) or in species-typical behavior (nest building) and no increased anxiety (open field, light-dark box) or depression/anhedonia (sucrose preference) at this relatively young age. These neurobehavioral deficits of the Fus1 KO mice at this relatively young age are highly relevant to sAD, making them suitable for effective research on pharmacological targets in the context of early intervention of sAD.