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The reproducibility crisis (or replication crisis) in biomedical research is a particularly existential and under-addressed issue in the field of behavioral neuroscience, where, in spite of efforts to standardize testing and assay protocols, several known and unknown sources of confounding environmental factors add to variance. Human interference is a major contributor to variability both within and across laboratories, as well as novelty-induced anxiety. Attempts to reduce human interference and to measure more \"natural\" behaviors in subjects has led to the development of automated home-cage monitoring systems. These systems enable prolonged and longitudinal recordings, and provide large continuous measures of spontaneous behavior that can be analyzed across multiple time scales. In this review, a diverse team of neuroscientists and product developers share their experiences using such an automated monitoring system that combines Noldus PhenoTyper ® home-cages and the video-based tracking software, EthoVision ® XT, to extract digital biomarkers of motor, emotional, social and cognitive behavior. After presenting our working definition of a “home-cage”, we compare home-cage testing with more conventional out-of-cage tests (e.g., the open field) and outline the various advantages of the former, including opportunities for within-subject analyses and assessments of circadian and ultradian activity. Next, we address technical issues pertaining to the acquisition of behavioral data, such as the fine-tuning of the tracking software and the potential for integration with biotelemetry and optogenetics. Finally, we provide guidance on which behavioral measures to emphasize, how to filter, segment, and analyze behavior, and how to use analysis scripts. We summarize how the PhenoTyper has applications to study neuropharmacology as well as animal models of neurodegenerative and neuropsychiatric illness. Looking forward, we examine current challenges and the impact of new developments. Examples include the automated recognition of specific behaviors, unambiguous tracking of individuals in a social context, the development of more animal-centered measures of behavior and ways of dealing with large datasets. Together, we advocate that by embracing standardized home-cage monitoring platforms like the PhenoTyper, we are poised to directly assess issues pertaining to reproducibility, and more importantly, measure features of rodent behavior under more ethologically relevant scenarios.

Fully integrative approach to the socibiology of caviomorph rodents   * Brings together research on social systems with that on epigenetic, neurendocrine and developmental mechanisms of social behavior * Describes the social systems of many previously understudied caviomorph species, identifying the fitness costs and benefits of social living in current day populations as well as quantified evolutionary patterns or trends   * Highlights potential parallels and differences with other animal models 

Animal behavior analysis software has become an essential tool in the life sciences. However, the currently available tools have some significant shortcomings that limit their use by individuals without programming skills, access to higher informatics resources, or the capability to invest large sums of money. We have developed and validated an easy-to-use and straightforward tracking system named ESTraS to address this issue. This freeware software allows researchers to track and analyze rodent behaviors, offering additional options such as trajectory and angle analysis. Through ESTraS, researchers can utilize unsupervised clustering techniques, such as k -means or hierarchical clustering, to further explore the obtained results. This clustering enables the classification of results based on observed similarities among subjects. The data of this manuscript shows that ESTraS can prove to be extremely valuable, not only by providing essential behavioral analysis tools but also by offering specific data analysis options with just one click.

Background Accurate determination of mouse positions from video data is crucial for various types of behavioral analyses. While detection of body positions is straightforward, the correct identification of nose positions, usually more informative, is far more challenging. The difficulty is largely due to variability in mouse postures across frames. Results Here, we present OptiMouse, an extensively documented open-source MATLAB program providing comprehensive semiautomatic analysis of mouse position data. The emphasis in OptiMouse is placed on minimizing errors in position detection. This is achieved by allowing application of multiple detection algorithms to each video, including custom user-defined algorithms, by selection of the optimal algorithm for each frame, and by correction when needed using interpolation or manual specification of positions. Conclusions At a basic level, OptiMouse is a simple and comprehensive solution for analysis of position data. At an advanced level, it provides an open-source and expandable environment for a detailed analysis of mouse position data.

There is increasing evidence that vascular risk factors, including aging, hypertension, diabetes mellitus, and obesity, promote cognitive impairment; however, the underlying mechanisms remain obscure. Cerebral blood flow (CBF) is adjusted to neuronal activity via neurovascular coupling (NVC) and this mechanism is known to be impaired in the aforementioned pathophysiologic conditions. To establish a direct relationship between impaired NVC and cognitive decline, we induced neurovascular uncoupling pharmacologically in mice by inhibiting the synthesis of vasodilator mediators involved in NVC. Treatment of mice with the epoxygenase inhibitor N-(methylsulfonyl)-2-(2-propynyloxy)-benzenehexanamide (MSPPOH), the NO synthase inhibitor l-NG-Nitroarginine methyl ester (L-NAME), and the COX inhibitor indomethacin decreased NVC by over 60% mimicking the aging phenotype, which was associated with significantly impaired spatial working memory (Y-maze), recognition memory (Novel object recognition), and impairment in motor coordination (Rotarod). Blood pressure (tail cuff) and basal cerebral perfusion (arterial spin labeling perfusion MRI) were unaffected. Thus, selective experimental disruption of NVC is associated with significant impairment of cognitive and sensorimotor function, recapitulating neurologic symptoms and signs observed in brain aging and pathophysiologic conditions associated with accelerated cerebromicrovascular aging.

Our understanding of laboratory animal behavior and the implications of husbandry activities on their wellbeing remains incomplete. This is especially relevant with an aging colony as their activity patterns may change as they mature. Home Cage Monitoring (HCM) provides valuable insights into mouse activity within the animal's own environment and can shed light on acclimatization periods and responses to husbandry activities such as cage changing. The aim of this study was to monitor and explore changes in the activity and rest disturbance (RDI) patterns of an aging colony of male and female C57/BL6 mice. The mice were housed in the Digitally Ventilated Cage system, for up to 18 months of age. Data was then downloaded to investigate how the activity patterns and RDI of the mice changed over time. Habituation, aging and cage change assessments were conducted using linear mixed models, while cage separation and stereotypic behavior investigations were conducted by visual inspection of the data. As expected during the study, mice were less active during the light phase compared to the dark phase. However, on arrival mice displayed heightened activity and RDI during the light phase and reduced activity and RDI during the dark phase, taking several days to adjust to baseline \"acclimatized\" patterns. With age, overall activity significantly decreased from 5 months until 14 months of age, after which it increased back toward baseline levels. We also observed activity spikes during our monitoring of this colony. Prolonged housing can lead to alarming stereotypic behaviors in animals. Cages of mice flagged for potential stereotypy displayed sustained activity spikes in the light and dark phases. Spikes in activity during the dark phase were much more pronounced than in the light phase. Cage changing led to an increase in the light phase activity and RDI compared to the previous day, with no observed difference in the dark phase post-cage change. This effect remained consistent as the animals aged. This study explores changes in the activity patterns of an aging colony of male and female C57/BL6 mice housed in the Digitally Ventilated Cage system. We identified distinct aging phases concerning activity and RDI differences and a potential new welfare application for the DVC , specifically for early detection of stereotypy. In conclusion, the adoption of HCM systems should be considered for long-term animal housing from both a welfare and behavioral perspective.

Automated observation and analysis of behavior is important to facilitate progress in many fields of science. Recent developments in deep learning have enabled progress in object detection and tracking, but rodent behavior recognition struggles to exceed 75–80% accuracy for ethologically relevant behaviors. We investigate the main reasons why and distinguish three aspects of behavior dynamics that are difficult to automate. We isolate these aspects in an artificial dataset and reproduce effects with the state-of-the-art behavior recognition models. Having an endless amount of labeled training data with minimal input noise and representative dynamics will enable research to optimize behavior recognition architectures and get closer to human-like recognition performance for behaviors with challenging dynamics.

Dietary supplementation with omega-3 (ω-3) fatty acids is a safe, economical mean of preventive medicine that has shown protection against several neurologic disorders. The present study tested the hypothesis that this method is protective against controlled cortical impact (CCI). Indeed, mice fed with ω-3 polyunsaturated fatty acid (PUFA)-enriched diet for 2 months exhibited attenuated short and long-term behavioral deficits due to CCI. Although ω-3 PUFAs did not decrease cortical lesion volume, these fatty acids did protect against hippocampal neuronal loss after CCI and reduced pro-inflammatory response. Interestingly, ω-3 PUFAs prevented the loss of myelin basic protein (MPB), preserved the integrity of the myelin sheath, and maintained the nerve fiber conductivity in the CCI model. ω-3 PUFAs also directly protected oligodendrocyte cultures from excitotoxicity and blunted the microglial activation-induced death of oligodendrocytes in microglia/oligodendrocyte cocultures. In sum, ω-3 PUFAs elicit multifaceted protection against behavioral dysfunction, hippocampal neuronal loss, inflammation, and loss of myelination and impulse conductivity. The present report is the first demonstration that ω-3 PUFAs protect against white matter injury in vivo and in vitro. The protective impact of ω-3 PUFAs supports the clinical use of this dietary supplement as a prophylaxis against traumatic brain injury and other nervous system disorders.

Mild traumatic brain injury (mild TBI) is a growing public concern, as evidence mounts that even brain injuries classified as “mild” can result in persistent neurological dysfunction. Multiple brain injuries heighten the likelihood of worsened or more prolonged symptomatology and may trigger long-term neurodegeneration. Animal models provide a logical platform to identify key parameters, such as loading forces, duration between injuries, and number of injuries, which contribute to additive or synergistic damage after repeated mild TBI. Despite the tremendous increase in research productivity in the field of repeated mild TBI, relatively few studies have been designed in such a way as to provide experimental-based insights into the dependence of cellular and functional outcomes on the prescribed parameters of mild TBI. In this review, we summarize how standard models of TBI have been adapted to produce mild TBI and highlight commonly observed aspects of neuropathology replicated in rodent models of mild TBI. The complexity of designing studies of repeated TBI is discussed, including challenges of incorporating appropriate control groups, informative experimental design, and relevant outcome measures. We then feature studies that provide a well-controlled, within-study design varying either the number of injuries or the interinjury interval. Harnessing the power of experimental models of TBI to elucidate which injury parameters are critical contributors to acute and chronic damage after repeated injury can further efforts at prevention and provide improved models for testing mechanisms and therapeutic interventions.

Existing assays of social interaction are suboptimal, and none measures propinquity, the tendency of rodents to maintain close physical proximity. These assays are ubiquitously performed using inbred mouse strains and mutations placed on inbred genetic backgrounds. We developed the automatable tube cooccupancy test (TCOT) based on propinquity, the tendency of freely mobile rodents to maintain close physical proximity, and assessed TCOT behavior on a variety of genotypes and social and environmental conditions. In outbred mice and rats, familiarity determined willingness to cooccupy the tube, with siblings and/or cagemates of both sexes exhibiting higher cooccupancy behavior than strangers. Subsequent testing using multiple genotypes revealed that inbred strain siblings do not cooccupy at higher rates than strangers, in marked contrast to both outbred and rederived wild mice. Mutant mouse strains with “autistic-like” phenotypes (Fmr1 −/y and Eif4e Ser209Ala) displayed significantly decreased cooccupancy.