Use of factorial designs to optimize animal experiments and reduce animal use

Optimization of experiments, such as those used in drug discovery, can lead to useful savings of scientific resources. Factors such as sex, strain, and age of the animals and protocol-specific factors such as timing and methods of administering treatments can have an important influence on the response of animals to experimental treatments. Factorial experimental designs can be used to explore which factors and what levels of these factors will maximize the difference between a vehicle control and a known positive control treatment. This information can then be used to design more efficient experiments, either by reducing the numbers of animals used or by increasing the sensitivity so that smaller biological effects can be detected. A factorial experimental design approach is more effective and efficient than the older approach of varying one factor at a time. Two examples of real factorial experiments reveal how using this approach can potentially lead to a reduction in animal use and savings in financial and scientific resources without loss of scientific validity.     

The scope for improving the design of laboratory animal experiments.

The factors which need to be taken into account in designing a 'good' experiment are reviewed. Such an experiment should be unbiased, have high precision, a wide range of applicability, it should be simple, and there should be a means of quantifying uncertainty (Cox 1958). The relative precision due to the use of randomized block designs was found to range from 96% to 543% in 5 experiments involving 30 variables. However, a survey of 78 papers published in two toxicology journals showed that such designs were hardly used. Similarly, designs in which more than one factor was varied simultaneously ('factorial designs') were only used in 9% of studies, though interactions between variables such as dose and strain of animal may be common, so that single factor experiments could be misleading. The consequences of increased within-group variability due to infection and genetic segregation were quantified using data published by G?rtner (1990). Both substantially reduced precision, but toxicologists continue to use non-isogenic laboratory animals, leading to experiments with a lower level of precision than is necessary. It is concluded that there is scope for improving the design of animal experiments, which could lead to a reduction in animal use. People using animals should be required to take formal training courses which include sessions on experimental design in order to minimize animal use and to increase experimental efficiency.     

ISOMORPHIC PERMUTED EXPERIMENTAL DESIGNS AND THEIR APPLICATION IN CONJOINT ANALYSIS

This paper deals with experimental designs used in conjoint analysis. The described approach permutes the structure of the underlying fractional experimental design to make different sets of combinations. The resulting experimental designs, suggested to be called Isomorphic Permuted Experimental Designs (IPED), are statistically equivalent to each other while combining diverse sets of the variables and levels into different designs. By facilitating distinctive individual designs (for each respondent), IPEDs reduce a bias caused by some possibly unusually strong performing combinations, and allow detection and estimation of interactions among variables, as well as identification of pattern-based segments emerging from individual models of utilities. This paper examines the theoretical foundation of the approach, formalizes the methodology for algorithmic implementation and shows a practical example of utilization.

PRACTICAL APPLICATIONS

Isomorphic Permuted Experimental Design (IPED) allows for overcoming multiple interlinked statistical problems that affect the traditional conjoint analysis approaches, thus leading to more reliable and targeted results in practice. IPED facilitates individual respondents' models based on unique designs, thus allowing for pattern-based segmentation. The approach also allows for the detection of any and all interactions between the elements (features) of the experiments, thus increasing the reliability of conjoint analysis results. It has been utilized in many practical applications, such as for message optimization, early stage new product development, advertising, package and website optimization.     

Reduction through education: the insight of a trainer

One of the articles contained within European Council Directive 86/609/EEC states that "Persons who carry out experiments or take part in them, and persons who take care of animals used for experiments, including duties of a supervisory nature, shall have appropriate training". In effect, this article stipulates that only competent individuals are allowed to work with laboratory animals. At least three groups of individuals can be identified with different responsibilities toward experimental animals: animal technicians, scientists, and veterinarians/animal welfare officers. The responsibilities and duties of the individuals within each of these categories differ. This paper focuses on the training of scientists. The scientist designs, and often also performs, animal experiments. Therefore, scientists must be educated to develop an attitude of respect toward laboratory animals, and must be trained so that, if an experiment must be performed with animals, it is designed according to the highest possible scientific and ethical standards. In The Netherlands, the law stipulates that scientists intending to work with animals must have completed a course in laboratory animal science. This compulsory course started in 1986. The Department of Laboratory Animal Science at Utrecht University is responsible for the national coordination of this course. Participants must have an academic degree (at the level of MSc) in one of the biomedical sciences, such as biology, medicine or veterinary medicine. Although the course is an intensive 3-week, 120-hour long course, which covers both technical and ethical aspects of laboratory animal experimentation, it cannot provide full competence. It is designed to provide sufficient basic training and knowledge to enable students to design animal experiments, and to develop an attitude that will be conducive to the implementation of the Three Rs. However, full competence will always require further training that can only be acquired as a result of practical experience gained while working in the field of laboratory animal research. Evaluations subsequent to the course have revealed that more than 98% of the students regard the course as indispensable for all scientists working in a research area where animal experiments are performed. They agree that the course not only contributes to the quality of experiments and to the welfare of animals, but also to a decrease in the number of animals used in experiments.     

Guidelines for the design and statistical analysis of experiments in papers submitted to ATLA

In vitro experiments need to be well designed and correctly analysed if they are to achieve their full potential to replace the use of animals in research. An "experiment" is a procedure for collecting scientific data in order to answer a hypothesis, or to provide material for generating new hypotheses, and differs from a survey because the scientist has control over the treatments that can be applied. Most experiments can be classified into one of a few formal designs, the most common being completely randomised, and randomised block designs. These are quite common with in vitro experiments, which are often replicated in time. Some experiments involve a single independent (treatment) variable, while other "factorial" designs simultaneously vary two or more independent variables, such as drug treatment and cell line. Factorial designs often provide additional information at little extra cost. Experiments need to be carefully planned to avoid bias, be powerful yet simple, provide for a valid statistical analysis and, in some cases, have a wide range of applicability. Virtually all experiments need some sort of statistical analysis in order to take account of biological variation among the experimental subjects. Parametric methods using the t test or analysis of variance are usually more powerful than non-parametric methods, provided the underlying assumptions of normality of the residuals and equal variances are approximately valid. The statistical analyses of data from a completely randomised design, and from a randomised-block design are demonstrated in Appendices 1 and 2, and methods of determining sample size are discussed in Appendix 3. Appendix 4 gives a checklist for authors submitting papers to ATLA.     

Evaluation of experimental designs for two-color cDNA microarrays.

The major goal of two-color cDNA microarray experiments is to measure the relative gene expression level (i.e., relative amount of mRNA) of each gene between samples in studies of gene expression. More specifically, given an N-sample experiment, we need all N(N - 1)/2 relative expression levels of all sample pairs of each gene for identification of the differentially expressed genes and for clustering of gene expression patterns. However, the intensities observed from two-color cDNA microarray experiments do not simply represent the relative gene expression level. They are composed of signal (gene expression level), noise, and other factors. In discussions on the experimental design of two-color cDNA microarray experiments, little attention has been given to the fact that different combinations of test and control samples will produce microarray intensities data with varying intrinsic composition of factors. As a consequence, not all experimental designs for two-color cDNA microarray experiments are able to provide all possible relative gene expression levels. This phenomenon has never been addressed. To obtain all possible relative gene expression levels, a novel method for two-color cDNA microarray experimental design evaluation is necessary that will allow the making of an accurate choice. In this study, we propose a model-based approach to illustrate how the factor composition of microarray intensities changed with different experimental designs in two-color cDNA microarray experiments. By analyzing 12 experimental designs (including 5 general forms), we demonstrate that not all experimental designs are able to provide all possible relative gene expression levels due to the differences in factor composition. Our results indicate that whether an experimental design can provide all possible relative expression levels of all sample pairs for each gene should be the first criterion to be considered in an evaluation of experimental designs for two-color cDNA microarray experiments.     

Pseudoreplication in experimental designs for the manipulation of seed germination treatments

In the published reports concerning the design of laboratory experiments examining signals that might trigger seed germination, there is currently a misunderstanding of what might constitute correct replication of the experimental treatment. This is particularly true for the study of dry heat, smoke and charcoal, where either an individual seed or a batch of seeds in a Petri dish or tray is being treated as the unit of replication of the experimental treatment, irrespective of whether or not those seeds were all subjected to the experimental manipulation simultaneously. Under these circumstances, the application of the treatment is unreplicated, while samples nested within that single application have been replicated, and the Petri dishes/trays are functioning solely as independent replicates of the variability in germination response within the seed batch used and variation within the pretreatment and post‐treatment environments. Thus any observed difference in germination may be due to the germination treatment but, potentially, it could also be due to any chance event affecting the treated sample. There are a number of alternative experimental designs that avoid this problem. The essential point with these designs is that the application of the experimental manipulation to each replicate should be separated in space by the use of separate experimental equipment and/or in time by the repeated use of the same experimental apparatus.     

Reducing sample size in experiments with animals: historical controls and related strategies

Reducing the number of animal subjects used in biomedical experiments is desirable for ethical and practical reasons. Previous reviews of the benefits of reducing sample sizes have focused on improving experimental designs and methods of statistical analysis, but reducing the size of control groups has been considered rarely. We discuss how the number of current control animals can be reduced, without loss of statistical power, by incorporating information from historical controls, i.e. subjects used as controls in similar previous experiments. Using example data from published reports, we describe how to incorporate information from historical controls under a range of assumptions that might be made in biomedical experiments. Assuming more similarities between historical and current controls yields higher savings and allows the use of smaller current control groups. We conducted simulations, based on typical designs and sample sizes, to quantify how different assumptions about historical controls affect the power of statistical tests. We show that, under our simulation conditions, the number of current control subjects can be reduced by more than half by including historical controls in the analyses. In other experimental scenarios, control groups may be unnecessary. Paying attention to both the function and to the statistical requirements of control groups would result in reducing the total number of animals used in experiments, saving time, effort and money, and bringing research with animals within ethically acceptable bounds.     

ENVIRONMENTAL EFFECTS ON ANIMALS USED IN BIOMEDICAL RESEARCH

I. Reliability of the results of bio-medical research clearly depends upon the animals used showing as standard responses as is possible.
2. The majority of animals used in this field are small, homoiothermic mammals which have sensitive and strong homeostatic mechanisms. If a change in ambient conditions is of sufficient magnitude to unbalance homeostasis, then the neuroendocrine system is stimulated so as to restore it, and this can interfere with the response to test conditions or agents.
3. The homeostatic effectors involved are diverse and can include both physiological and behavioural changes in the animal. These can affect metabolic rate, body temperature, activity, food consumption, hormone concentration, wake/sleep patterns, maturation, posture, lactation and many other bodily functions. Any of these changes is potentially capable of influencing experimental results.
4. The evidence presented shows how environmental factors may affect the outcome of experiments in the fields of animal behaviour, cancer research, immunology, pathology, pharmacology, psychology, reproduction, teratology and toxicology; particular attention is paid to the effects of ambient temperature, relative humidity, air movement and quality, light and sound.
5. While a constant, reproducible environment would be ideal, there is little possibility of controlling all the variables; nevertheless all investigators should minimize those environmental variables that have been shown to be important.
6. To enable other investigators to repeat experiments or carry out comparative studies, environmental conditions pertaining during an experiment should be adequately described in any publications.     

Impact of environmental enrichment in mice. 1: effect of housing conditions on body weight,organ weights and haematology in different strains

Currently, environmental enrichment is a very common means of improving animal well-being, especially for laboratory animals. Although environmental enrichment seems to be a possible way for improving the well-being of animals, the consideration of housing laboratory animals should not only focus solely on animal well-being, manpower and economics but also on the precision and accuracy of the experimental results. The purpose of the present study was to evaluate the effects of enriched cages (nest box, nesting material, climbing bar) on body weight, haematological data and final organ weights. BALB/c, C57BL/6 and A/J mice, originated from Harlan Winkelmann, were used for the experiments - 16 animals of each strain. Animals at 3 weeks of age were marked and separated randomly to enriched or non-enriched cages, in groups of four, half for each housing condition. Both cages were type III Makrolon cages, only the enriched cages contained a nest box, a wood bar for climbing and nesting material. Animals were kept in a clean animal room under specific pathogen free (SPF) conditions. Body weights were recorded every week. Blood samples were collected at 14 weeks of age (white blood cells (WBC), red blood cells (RBC), haemoglobin (HGB), and haematocrit (HCT) were analysed). At 15 weeks of age, the animals were euthanized by CO(2) in their home cages, and final body weight and organ weights (heart, liver, kidney, adrenal, spleen and uterus) were recorded immediately. Although nearly all the test variables were not affected by environmental enrichment in their mean values, the enriched group showed higher coefficients of variation in many variables, and strain differences of both housing conditions were not consistent. The influences of enrichment were shown to be strain- and test-dependent. Such effects may lead to an increase in the number of animals which is necessary or may change the experimental results, especially when a study, using enriched housing conditions, focuses on strain differences. Since the same enrichment design can result in different influences, a positive or a negative or no adverse effect, due to the strain and the variables studied, researchers need to collect more information before enrichment designs are introduced into experimental plans.     

Like moths to a street lamp: exaggerated animal densities in plot‐level global change field experiments

Many recent field experiments have examined plant responses to global change factors such as climate warming, elevated atmospheric CO₂, increased nitrogen addition or altered precipitation simulated at the plot level, yet the mechanisms underlying these responses can be difficult to isolate. One concern has been that the infrastructure used in these experiments can restrict the access of influential herbivores, detritivores or pollinators to the plots, and the absence of these animals is confounded with the treatment effects. However, in this paper we describe why free access by animals to experimental plots does not ensure realistic animal densities in response to global change treatments. On the contrary, much like moths swarm around streetlamps, animals that prefer the local conditions in treated plots may congregate at artificially high densities, or conversely, those that are repelled by the treatments may choose to avoid them. Therefore, animal densities or herbivore damage in the plots of global change experiments may grossly exaggerate or underestimate the contributions of animals to primary productivity or plant species composition under future environmental conditions. We describe how these potential animal congregation and avoidance artifacts may have been overlooked in the interpretation of results from many plot‐level global change field experiments. We also provide suggestions for how to best interpret the results of these experiments and how to isolate the effects of animal density artifacts.     

Are animal models as good as we think?

Models have been a tool of science at least since the 18th century and serve a variety of purposes from focusing abstract thoughts to representing scaled down version of things for study. Generally, animal models are needed when it is impractical or unethical to study the target animal. Biologists have taken modeling by analogy beyond most other disciplines, deriving the relationship between model and target through evolution. The "unity in diversity" concept suggests that homology between model and target foretells functional similarities. Animal model studies have been invaluable for elucidating general strategies, pathways, processes and guiding the development of hypotheses to test in target animals. The vast majority of animals used as models are used in biomedical preclinical trials. The predictive value of those animal studies is carefully monitored, thus providing an ideal dataset for evaluating the efficacy of animal models. On average, the extrapolated results from studies using tens of millions of animals fail to accurately predict human responses. Inadequacies in experimental designs may account for some of the failure. However, recent discoveries of unexpected variation in genome organization and regulation may reveal a heretofore unknown lack of homology between model animals and target animals that could account for a significant proportion of the weakness in predictive ability. A better understanding of the mechanisms of gene regulation may provide needed insight to improve the predictability of animal models.     

Control of laboratory acquired hemorrhagic fever with renal syndrome (HFRS) in Japan

By the end of 1985, 126 human cases of laboratory acquired hemorrhagic fever with renal syndrome (HFRS) were recorded in Japan. Seroepidemiological studies revealed that laboratory rats exhibited high IFA titers against Hantaan or related viruses at locations where HFRS patients occurred. Laboratory researchers contracted HFRS more frequently than laboratory animal technicians or caretakers, although a laboratory animal caretaker died of the disease. Inhalation of HFRS-virus contaminated air in an animal facility is the likely cause of infection with this virus. Wound infection during animal experiments may be another important route of infection. Infection of laboratory rats can occur by transferring animals from contaminated to other animal facilities. Tissue fragments or cells of transplantable animal tumors are a potential source of spreading the HFRS virus. Eradication of HFRS virus from a contaminated animal facility can be achieved best by elimination of all animals in the room, especially when human HFRS is associated with an infected colony. In some cases, when IFA titers of the sera of the rats tested were low, infection apparently disappeared without instituting any particular control measures other than ordinary procedures for care and management of laboratory animals. HFRS viruses have not yet been eradicated from all animal facilities in Japan. Therefore, serological monitoring of laboratory rats continues.     

Sequentially Generated Designs

Procedures for sequential generation of nearly D-optimal designs are described. Two kinds of designs can be obtained: symmetrical block designs and nonsymmetrical ones. It is shown that in a special case when the number of the support points of a continuous D-optimal design equals to the number of regression coefficients the sequential designs can be constructed very easy without use of a computer. A Catalogue containing 135 designs has been developed by use of these procedures. 34 of them can be used for experiments in cuboidal factor space and the remaining for experiments with mixture and process variables. Comparison with other designs is done.     

A Common Control Group - Optimising the Experiment Design to Maximise Sensitivity

Methods for choosing an appropriate sample size in animal experiments have received much attention in the statistical and biological literature. Due to ethical constraints the number of animals used is always reduced where possible. However, as the number of animals decreases so the risk of obtaining inconclusive results increases. By using a more efficient experimental design we can, for a given number of animals, reduce this risk. In this paper two popular cases are considered, where planned comparisons are made to compare treatments back to control and when researchers plan to make all pairwise comparisons. By using theoretical and empirical techniques we show that for studies where all pairwise comparisons are made the traditional balanced design, as suggested in the literature, maximises sensitivity. For studies that involve planned comparisons of the treatment groups back to the control group, which are inherently more sensitive due to the reduced multiple testing burden, the sensitivity is maximised by increasing the number of animals in the control group while decreasing the number in the treated groups.     

Selection of best conditions of inoculum preparation for optimum performance of the pigment production process by Talaromyces spp. using the Taguchi method

Process optimisation techniques increasingly need to be used early on in research and development of processes for new ingredients. There are different approaches and this article illustrates the main issues at stake with a method that is an industry best practice, the Taguchi method, suggesting a procedure to assess the potential impact of its drawbacks. The Taguchi method has been widely used in various industrial sectors because it minimises the experimental requirements to define an optimum region of operation, which is particularly relevant when minimising variability is a target. However, it also has drawbacks, especially the intricate confoundings generated by the experimental designs used. This work reports a process optimisation of the synthesis of red pigments by a fungal strain, Talaromyces spp. using the Taguchi methodology and proposes an approach to assess from validation trials whether the conclusions can be accepted with confidence. The work focused on optimising the inoculum characteristics, and the studied factors were spore age and concentration, agitation speed and incubation time. It was concluded that spore age was the most important factor for both responses, with optimum results at 5 days old, with the best other conditions being spores concentration, 100,000 (spores/mL); agitation, 200 rpm; and incubation time, 84 h. The interactive effects can be considered negligible and therefore this is an example where a simple experimental design approach was successful in speedily indicating conditions able to increase pigment production by 63% compared to an average choice of settings. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:621–632, 2017     

Parasites in hybridizing communities: the Red Queen again?

Over the past two decades, infection levels in hybrids have frequently been compared with those in their progenitor species to find out whether parasites favour or penalize hybridization. Four static infection scenarios are possible, depending on whether hybrid resistance differs from that of one or both parental species. All four alternatives have been supported by some empirical data, but any potential dynamics might have been overlooked because of limited sampling or experimental designs. However, coevolutionary oscillations generated by frequency-dependent selection might provide a better explanation for the observed results than does a static genetic perspective of host resistance.     

The impact of huts on physiological stress: a refinement in post-transport housing of male guineapigs (Cavia porcellus)

The ideal animal model would contribute no confounding variables in experimental science. Variables affect experimental design resulting in increased animal use or repeated studies. We demonstrated a simple refinement which may reduce the number of animals used experimentally while simultaneously improving animal welfare. The objective of this study was to determine if the presence of a hut was an impact on physiological stress levels, as determined by faecal cortisol concentration, during a routine four-day acclimatization period of newly received male Hartley-Outbred guineapigs. We hypothesized that those animals provided with huts would have decreased physiological stress compared with animals not provided with huts. We examined this effect within both paired and single-housed animals. A between-subjects one-way analysis of variance revealed that pair-housed animals with a hut had significantly lower faecal cortisol concentration than pair-housed animals without a hut and the presence and absence of a hut had no significant impact on faecal cortisol concentration in single-housed animals. These findings show that presence of a hut is beneficial in reducing physiological stress when pair housing male guineapigs and does not appear to have an impact when single housing male guineapigs. In addition, we have shown that faecal cortisol, and therefore physiological stress, is still increasing on study day 4 suggesting a longer acclimatization period is necessary. A simple refinement in housing environment and acclimatization time can both reduce the number of animals used experimentally and improve animal welfare.     

Research with animals: requirement, responsibility, welfare

Recognition of unacceptable cruelty to animals in pasttimes such as bull-baiting, dates in Britain from the early 19th century. The Society for the Prevention of Cruelty to Animals was founded in 1824. Several bills to curb cruelty were discussed in Parliament, and the Cruel and Improper Treatment of Cattle Act was passed in 1822. Other Acts have followed over the years. Cruelty in the form of painful scientific experiments, including dissection of living, conscious animals, vivisection, was proscribed by the Cruelty to Animals Act 1876. That Act required anyone wishing to experiment with animals to obtain a licence from the Secretary of State. Conditions for issue of licences were strict and remain so to this day. The Act is still valid, and is enforced by the Home Office, with its medical and veterinary Inspectors. The Cruelty to Animals Act 1876 allows experiments on animals under strictly controlled conditions. Experiments must have the clear objective of improving the welfare of man and/or animals. Benefits from experiments carried out under the Act have been enormous, covering every aspect of diagnosis, treatment, and prophylaxis in human and veterinary medicine. Coincidentally, the welfare of laboratory animals has also been greatly improved. There has always been some opposition to the use of animals in biomedical research. The subject is emotive but, by and large, discussion has been rational and within the law. In recent years, however, the morality of using experimental animals has been examined more closely. The possibility of replacing them by alternative methods has been investigated. Where these alternatives are applicable, they are used and further research on them continues. The questioning of animal experiments has emphasized the need to look constantly at animal welfare to ensure humane treatment of all animals, especially those restricted in a laboratory or on a farm. Attention has been drawn in this work to our existing laws protecting animals, but new legislation is being demanded, not only by some lay welfare groups but also by scientists. Hence, it has become very important to discuss various ways of ensuring animal welfare, including by legislation, especially with those knowledgeable in laboratory animal science and animal experiments.(ABSTRACT TRUNCATED AT 400 WORDS)