Protocol for a systematic review of guidelines for rigour in the design, conduct and analysis of biomedical experiments involving laboratory animals

Objective: Within the last years, there has been growing awareness of the negative repercussions of unstandardized planning, conduct and reporting of preclinical and biomedical research. Several initiatives have set the aim of increasing validity and reliability in reporting of studies and publications, and publishers have formed similar groups. Additionally, several groups of experts across the biomedical spectrum have published experience and opinion-based guidelines and guidance on potential standardized reporting. While all these guidelines cover reporting of experiments, an important step prior to this should be rigours planning and conduction of studies. The aim of this systematic review is to identify and harmonize existing experimental design, conduct and analysis guidelines relating to internal validity and reproducibility of preclinical animal research. The review will also identify literature describing risks of bias pertaining to the design, conduct and analysis of preclinical biomedical research. Search strategy: PubMed, Embase and Web of Science will be searched systematically to identify guidelines published in English language in peer-reviewed journals before January 2018 (box 1). All articles or systematic reviews in English language that describe or review guidelines on the internal validity and reproducibility of animal studies will be included. Google search for guidelines published on the websites of major funders and professional organisations can be found in (Box 2). Screening and annotation: Unique references will be screened in two phases: screening for eligibility based on title and abstract, followed by screening for definitive inclusion based on full text. Screening will be performed in SyRF (http://syrf.org.uk). Each reference will be randomly presented to two independent reviewers. Disagreements between reviewers will be resolved by additional screening of the reference by a third, senior researcher. Data management and reporting: All data, including extracted text and guidelines, will be stored in the SyRF platform. Elements of the included guidelines will be identified using a standardized extraction form. Reporting will follow the PRISMA guidelines as far as applicable

Effect of Population Heterogenization on the Reproducibility of Mouse Behavior : A Multi-Laboratory Study

Peer reviewe

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Breakdown of the ideal free distribution under conditions of severe and low competition

Under the ideal free distribution (IFD), the number of organisms competing for a resource at different sites is proportional to the resource distribution among sites. The ideal free distribution of competitors in a heterogeneous environment often predicts habitat matching, where the relative number of individuals using any two patches matches the relative availability of resources in those same two patches. If a resource is scarce, access might be restricted to individuals with high resource holding potential, resulting in deviation from the IFD. The distribution of animals may also deviate from the IFD in the case of resource abundance, when social attraction or preference for specific locations rather than competition may determine distribution. While it was originally developed to explain habitat choice, we apply the habitat matching rule to microscale foraging decisions. We show that chickens feeding from two nondepleting feeders distribute proportionally to feeder space under intermediate levels of competition. However, chicken distribution between the feeders deviates from the IFD when feeder space is limited and competition high. Further, despite decreasing aggression with increasing feeder space, deviation from IFD is also observed under an excess supply of feeder space, indicating different mechanisms responsible for deviations from the IFD. Besides demonstrating IFD sensitivity to competition, these findings highlight IFD's potential as a biological basis for determining minimal resource requirements in animal housing.Significance statementThe ideal free distribution (IFD) predicts how animals ought to distribute themselves within a habitat in order to maximize their payoff. Recent studies, however, have questioned the validity of the IFD concept following anomalous results. We studied the IFD in chickens by systematically varying the amount and distribution of space at two feed troughs. We show that when tested over a sufficiently large range, the distribution of birds depends on the overall resource availability. Furthermore, behavioral data suggest that distinctly different mechanisms account for deviations from the IFD at shortage and excess supply of feeder space, respectively

Physical Health Problems and Environmental Challenges Influence Balancing Behaviour in Laying Hens.

With rising public concern for animal welfare, many major food chains and restaurants are changing their policies, strictly buying their eggs from non-cage producers. However, with the additional space in these cage-free systems to perform natural behaviours and movements comes the risk of injury. We evaluated the ability to maintain balance in adult laying hens with health problems (footpad dermatitis, keel damage, poor wing feather cover; n = 15) using a series of environmental challenges and compared such abilities with those of healthy birds (n = 5). Environmental challenges consisted of visual and spatial constraints, created using a head mask, perch obstacles, and static and swaying perch states. We hypothesized that perch movement, environmental challenges, and diminished physical health would negatively impact perching performance demonstrated as balance (as measured by time spent on perch and by number of falls of the perch) and would require more exaggerated correctional movements. We measured perching stability whereby each bird underwent eight 30-second trials on a static and swaying perch: with and without disrupted vision (head mask), with and without space limitations (obstacles) and combinations thereof. Video recordings (600 Hz) and a three-axis accelerometer/gyroscope (100 Hz) were used to measure the number of jumps/falls, latencies to leave the perch, as well as magnitude and direction of both linear and rotational balance-correcting movements. Laying hens with and without physical health problems, in both challenged and unchallenged environments, managed to perch and remain off the ground. We attribute this capacity to our training of the birds. Environmental challenges and physical state had an effect on the use of accelerations and rotations to stabilize themselves on a perch. Birds with physical health problems performed a higher frequency of rotational corrections to keep the body centered over the perch, whereas, for both health categories, environmental challenges required more intense and variable movement corrections. Collectively, these results provide novel empirical support for the effectiveness of training, and highlight that overcrowding, visual constraints, and poor physical health all reduce perching performance