Chapter 019, Taxonomy and History (American College of Laboratory Animal Medicine)

Handbook of Laboratory Animal Management and Welfare
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Molecular epidemiology of leishmaniasis in Asia focus on cutaneous infections. Infect Dis. Cutaneous leishmaniasis caused by Leishmania L. Isolation of antibabesial compounds from Brucea javanica, Curcuma xanthorrhiza, and Excoecaria cochinchinensis. Evaluation of efficacy of bruceine A, a natural quassinoid compound extracted from a medicinal plant, Brucea javanica, for canine babesiosis. Evaluation of Echinococcus multilocularis tetraspanins as vaccine candidates against primary alveolar echinococcosis.

Multiplex PCR system for identifying the carnivore origins of faeces for an epidemiological study on Echinococcus multilocularis in Hokkaido, Japan. Parasitol Res. Molecular cloning and characterization of a Tlike protein in Echinococcus multilocularis. Monitoring of environmental contamination by Echinococcus multilocularis in an urban fringe forest park in Hokkaido, Japan.

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Health Prev. A vague understanding of the biology and epidemiology of echinococcosis by dog owners in Hokkaido, an endemic island for Echinococcus multilocularis in Japan. Echinococcus multilocularis infection in pet dogs in Japan. Abdominal cysticercosis in a cynomolgus monkey.

Prevalence of Trichinellosis in wildlife of Hokkaido, and the taxonomy. Analysis of expressed sequence tags from the four main developmental stages of Trypanosoma congolense. A field study to estimate prevalence of bovine African trypanosomosis in Butaleja district, Uganda. Brucea javanica. Kamiya M. Taenia taeniaeformis : Colonic hyperplasia in heavily infected rats. Taenia taeniaeformis : Fate and proliferation of mucosal cells during gastric hyperplasia in larvae infected rats.

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Leishmaniasis in Sindh, Pakistan: outbreak and review of the literature. Rakuno Gakuen Univ. Improvement of copro-DNA detection for diagnosis in prepatent period of Echinococcus multilocularis infection in dogs. The use of tetracycline in anthelmintic baits to assess baiting rate and drug efficacy against Echinococcus multilocularis in foxes. Echinococcosis risk among domestic definitive hosts, Japan. Research on targeting sources of alveolar echinococcosis in Japan. Epizootiological survey of Trichinella spp.

The vaccination potential of EMY antigen against Echinococcus multilocularis infection. Genetic uniformity of Echinococcus multilocularis collected from different intermediate host species in Hokkaido, Japan. Control trial against Echinococcus multilocularis by local residents. Analysis of Leishmania proteins for the serodiagnosis of cutaneous leishmaniasis in Pakistan. Cysticercus tenuicollis infection in a cynomolgus monkey.

In: Shuyoshojyo-wo-kisonishita-inu-no-rinsho. Maede, Y. Hookworm infection. Roundworm infection. In: Shuyoshojyowo-kisonishita-inu-no-rinsho. Trichomonad enteritis. Amoebic enteritis. Whipworm infection. Esophageal worm disease. In: Saishin-kachiku-kiseichubyo-gaku. Itagaki, H. Cestode infection in domestic fowls. Cestode infection in ruminants. Cestode infection in horses. Current status of Echinococcus, a zoonotic parasite. Cestode infection.

Iwaki, T. A control trial for echinococcosis in Hokkaido, perspectively driven by local residents. Parasitic helminthes from feral raccoons Procyon lotor in Japan. Helminthologia , Current control strategies targeting sources of echinococcosis in Japan. Enhancement of splenic glucose metabolism during acute malarial infection : correlation of findings of FDG-PET imaging with pathological changes in a primate model of severe human malaria.

Identification of animals excreting feces collected in field for epizootiological studies of echinococcosis. Amebic colitis. Schistosomiasis japonica. A servey of gastrointestinal parasites in dogs and cats in Kanto district. Canine echinococcosis and its diagnosis. Anoplocephala sp. Planta Med. Phytochemistry , Hokkaido Hyakka , 4: Parasitology , Influence of H2 complex and non-H2 genes on progression of cutaneous lesions in mice infected with Leishmania amazonensis. FEBS Lett. Control program against hydatidosis and the decreased prevalence in Uruguay. Canine Echinococcosis.

In Japanese. Effective countermeasures against alveolar echinococcosis in red fox population of Hokkaido, Japan. Ear mite infection.

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List of major gastrointestinal parasite infections. Annual report of Uehara Moemorial Bioscience Foundation, Taenia solium, T. Parasitic zoonosis. Current status of leushmaniasis in the world and Japan. Parasite information system useful for routine diagnosis. Therapy, Chapter III 5. Mongolian J. Prevention of alveolar echinococcosis? Acta Tropica, In Japanese with English abstract. Control and management of parasitic zoonoses maintained in wildlife : A trial of Hokkaido University against echinococcosis. Nakamura M, Lee KJ eds. Countermeasures against animal infections protect human infection.

Modern Vet. Echinococcosis in Japan and its countermeasures. Kansensho, Current status and its countermeasures. Rinshoi, Kansensho to Kagaku-Ryoho, Parasitology, Retarded gastric acid secretion in rats infected with larval Taenia taeniaeformis. Res, Endoparasites of three species of house geckoes in Lampung, Indonesia. The present status of the Tarim red deer in Xinjiang, China. Biosphere Conservation, 4: Present situation of echinococcosis in Hokkaido. Diagnosis of the definitive hosts and control of the infectious source for human.

Hokkaido Vet. How can we prevent alveolar echinococcosis? Ecosystem and risk management a viewpoints. Trichinellosis in swine. Fecal examination of three species of carnivores in Koshimizu town in Hokkaido, Japan, for the epidemiology of alveolar echinococcosis. Toyamadaigaku-Kyoikugakubu-Kenkyuronbunshu, 5: In: Zoonosis Control, Bayer, Pathogen expanding with host movement.

Current situation of zoonosis 3 Echinococcosis. Kansen to Kokinyaku, Learn the zoonosis - 2nd talk: Echinococcosis First part. Aigandoubutsu, J Learn the zoonosis - 3rd talk: Echinococcosis Second part.

Review of Medical and Veterinary Mycology

Aigandoubutsu, Parasitic nematodes and acanthocephalan obtained from wild murids and dipodids captured in Xingiang-Uygur, China. Biogeography , 3: Collection record of small mammals in Xinjiang-Uygur, and with brief review of its mammalian fauna. Inhabitory of different UV lamps on the infectivity of taeniid eggs.

Seroprevalence of Borna disease virus in domestic animals in Xinjiang, China. A preliminary study of the genetic diversity of Xingiang Tarim red deer Cervus elaphus yarkandensis using the microsatellite DNA method. Jpn J Vet. A survey of canine echinococcosis in Gobi Altai Province of Mongolia by coproantigen detection. J Vet.

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Parasitic helminths from amphibians and reptiles in Osaka Municipal Tennoji Zoo. Zoo Wildl. In: Helminths of Wildlife, N. Chowdhury and A. Aguirre, Editors. Science Publishers, Inc. Parasitic zoonoses 1 Echinococcosis, Control for the definitive hosts. Kagaku-Ryoho-no-Ryoiki, Parasites in the environment. Echinococcosis multilocular and alveolar hydatid disease in Hokkaido Japan. Whilst our findings apply to this sample of papers, our results may in fact underestimate the extent of the reporting omissions.

In fact, the search retrieved papers from a range of publication years — , covering a wide variety of research areas, and an extensive range of journals across the impact factor spectrum, including Nature and Science. Whilst it would be useful to know if there is a relationship between the quality of the papers surveyed and the impact factors of the journals they were published in, this analysis was not in the remit of this survey.

Scientific papers should report sufficient relevant information about the experimental objectives, animal characteristics, experimental methods used and results obtained, in order to critically assess the findings and both the scientific and ethical implications of a study, or to allow the work to be repeated. Surprisingly, some of the studies surveyed either did not describe the purpose of the study at all or it was unclear to the assessors, and thus presumably also to any non-specialist reader. In addition, in some of the studies surveyed it was unclear whether one or more experiments were being described, and the experimental unit e.

Many of the studies surveyed omitted details about the strain, sex, age and weight of the animals used. These are all factors that can potentially influence experimental results and are therefore scientifically important [9] — [11]. This information is generally readily available to researchers and can be succinctly described, so it is unclear why omitting these essential details is so prevalent. Many journals offer supplementary online space generally unlimited not only for methodological information but also for additional results and tables. This information resource was considered, where it was available, for the papers surveyed.

The availability of this resource negates the argument that the lack of detail in published papers is primarily due to a lack of space. Studies have found that some experimental details such as chemical interactions and equipment are extensively discussed in the body of the paper, whilst information about animal characteristics, sample sizes etc are scantily provided or are absent [10] , [11]. In some of the included publications, the number of animals used was not reported anywhere in the methods or the results sections.

Reporting animal numbers is essential so that the biological and statistical significance of the experimental results can be assessed or the data re-analysed, and is also necessary if the experimental methods are to be repeated. Crucially, none of the studies assessed in more detail discussed how the sample size was chosen. Power analysis or other very simple calculations, which are widely used in human clinical trials and are often expected by regulatory authorities in some animal studies, can help to determine an appropriate number of animals to use in an experiment in order to detect a biologically important effect if there is one [3] , [12].

Handbook of Laboratory Animal Management and Welfare

This is a scientifically robust and efficient way of determining animal numbers and may ultimately help to prevent animals being used unnecessarily. Many of the studies that did report the number of animals used reported the numbers inconsistently between the methods and results sections.

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The reason for this is unclear, but this does pose a significant problem when analysing, interpreting and repeating the results. The assessment of experimental design found that random allocation of animals to treatment groups was reported in only a very small proportion of all the studies surveyed.

Randomisation reduces selection bias, increases the validity of the findings and, in principle, is always an appropriate and desirable aspect of good experimental design when two or more treatments are compared [3]. Randomised block designs — where the experimental animals are first divided into groups before the groups are randomly assigned to a treatment group — can be used to introduce variation in the groups of animals e. We cannot rule out that some of the studies surveyed may have used randomisation where appropriate, but did not report using it. If this was the case, then this kind of reporting omission can easily be rectified.

But if not, incomplete reporting masks potentially flawed experimental methods. Blinded assessment, where appropriate, minimises any bias in the qualitative scoring of subjective experimental observations, improving the rigour of the experimental method and the scientific validity of the results obtained, and yet blinding is rarely reported as being performed [3].

It cannot be ruled out that a proportion of the studies may indeed have used blinding but did not report it. Reviews of animal research in the field of emergency medicine found that studies which did not use randomisation and blinding to reduce bias when comparing two or more experimental groups, were significantly more likely to find a difference between the treatment groups [15] , [16]. Those studies that did incorporate these measures gave a lower estimate of treatment efficacy, meaning that the treatment effects were more likely to be accurately estimated.

These findings indicate that experimental designs which minimise bias have implications for the robustness of scientific results and, in biomedical research, the suitability of these animal studies for translation into clinical trials. Statistical methods are important for calculating the degree of confidence in, for example, the reproducibility and general validity of experimental results, and were used and reported by the majority of studies.

The majority of the studies that used and described a statistical method were judged to have used a correct statistical method. Whilst the majority of papers that used a statistical method described it and reported the numerical results with an error measure, many papers did not. Reporting the statistical method used together with an indication of the measure of variation or uncertainty is essential for interpreting any results, and has implications for the reliability and generalisability of the findings to other species and systems external validity [3] , [17].

In many papers, due to the lack of information detailing the statistical methods it was difficult to judge whether or not the statistical analysis were appropriate, or if data had been efficiently extracted and analysed. These issues are not new, as previous surveys of publications describing animal research and assessing specific aspects of experimental design, statistical analysis and reporting, have shown [7] , [8] , [11] , [18] , [19]. Data omissions and errors in presentation were other common findings.

The author concluded that the quality of reporting, experimental design and statistical analysis in reports of scientific research could be improved. The problems with experimental design and reporting that we have identified are also in line with similar reviews of the literature in various other scientific and clinical research areas [18] — [25].

In these research areas too, the quality of reporting and experimental design has been found wanting. The entire scientific community is reliant on published experiments being appropriately designed and carried out, and accurately and transparently reported, as this has implications for the scientific validity of the results.

Standards developed for reporting clinical research have improved the quality and transparency of reporting of clinical trials and have been adopted by many leading medical journals as part of their instructions to authors [26] , [27]. Reporting guidelines have also been developed for other specific research areas [28] — [33].

However, most biomedical journals currently provide little or no guidance about how to report research using animals apart from the ethical considerations regarding the procedures used. We believe that there is a need to develop reporting standards specifically for research using animals, and to provide guidance on the relevant information that should be included, with the aim of enhancing the transparency of reporting and encouraging both researchers, and those journals responsible for publishing this research, to adopt and adhere to them.

This is the largest and most comprehensive survey of this kind carried out to date. We provide evidence that many peer-reviewed, animal research publications fail to report important information regarding experimental and statistical methods. Whilst our findings are limited to experimental studies using rodents and primates carried out in UK and US laboratories, this is the statistical population that dominates the biomedical research literature, so our results are important and indeed, indicate cause for concern. Scientific publication is the method by which research has traditionally been described and the results communicated and it remains a powerful and important source of information.

The authors of scientific publications therefore have a responsibility to describe their experimental and statistical methods and results comprehensively, accurately and transparently, and journal editors share the responsibility to ensure that published studies fulfil these criteria. This is particularly pertinent for research involving animals, as poorly designed and reported experiments raise ethical as well as scientific concerns.

Whilst we recognise that in some studies, not all of the details we assessed e. We are simply arguing for the inclusion of all relevant information that will allow a suitably skilled reader to assess, analyse, and repeat the study's findings. There are many opportunities for the scientific community to improve both the experimental design and the quality of reporting of biomedical research using animals.

Serious efforts are needed to improve both the quality of experimental design and the quality of reporting in order to make research articles better suited to the needs of readership. The NC3Rs has identified a number of ways of helping to make these improvements. Raising awareness that these problems exist will be the first step in tackling these fundamental issues.

In addition, working with researchers, journal editors and funding bodies, the NC3Rs is building on the results of this survey by developing a set of reporting guidelines to assist researchers, journal editors and research funding bodies to take appropriate steps to improve the quality and transparency of reporting in the scientific publications with which they are associated. See supplementary online information for search terms. An upper limit on the number of papers that would be included in the survey was set at — made up of approximately 50 papers for each of three species and two countries.

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This limit was based on pragmatic considerations that included the time taken to assess and extract information from each publication. The sample size for surveys such as this is not normally based on formal statistical considerations, as there are no primary hypotheses being tested. There was therefore no need to formally power this study. A sample of the most recently indexed abstracts was selected from the total number of potentially relevant publications identified in the database search. When a journal is added to a database and becomes indexed, all previous issues are also indexed, enabling us to have a spread of publication years in the sample.

The abstracts were appraised and publications were selected or rejected based on the exclusion criteria listed below see Figure 1. The full texts of the remaining publications were obtained. Each potentially relevant full text was numbered within its country-species stratum and the exact reference of each paper recorded. This stratified randomisation procedure was carried out to minimise bias, to ensure the total sample was representative of the six subgroups i. The first fifty papers for each species and country were considered from each of the six randomised lists.

If a paper was not eligible, the next paper on the randomised list was taken. A second reviewer independently assessed the full texts of all the selected papers and finalised the list of included studies. Some further studies were excluded in this step. Studies whose funding source was not stated were included only if the research was carried out at a UK or USA publicly funded institution. Note was made that the funding source information was not reported. We chose to limit our investigation to publicly funded research in the USA and UK because the funding for this study came from both US and UK publicly funded bodies, the two countries are highly influential in setting the scientific agenda, and because there should theoretically be no constraints on reporting publicly funded research for reasons of confidentiality or commercial sensitivity.

The survey was restricted to original scientific research studies using mice, rats, and primates. The experiments had to use live animals including terminal anaesthesia and state that they had used UK Animals [Scientific Procedures] Act ASPA licensed interventions, or equivalent USA institutional guidelines for animal care and use.

Other species or groups such as fish, birds, rabbits and guinea-pigs are either used in small numbers or in more specialised areas of research. The sample sizes for these species would have been too small to draw any strong inferences about the reporting standards in these research areas. In addition, every such study that was included would reduce the statistical power of the study for drawing inferences about reporting and experimental design standards studies involving more widely used species. No more than two papers were included from any single laboratory to ensure that the survey results were not unduly influenced by the bad — or good — practice of one particularly productive laboratory.

Many papers report the results of more than one experiment; accordingly, the number of experiments per paper was noted. Details and results from the main experiment were used to complete the data collection sheets. Although the specific details described in this report relate to a single experiment assessed in each publication, the whole paper was searched for information relevant to that experiment, and to the way the experimental work was conducted and analysed in general. In phase 1, the full texts of the included studies were divided equally between two assessors who were experienced statisticians one from the UK and one from the USA.

Assessor 1 analysed the even numbered papers, assessor 2 analysed the odd numbered papers extracting the relevant information to complete the Quality of Reporting checklist see Supporting Information S1. Any supplementary online data associated with any of the included publications was accessed and analysed. In phase 2, a random sub-sample of 48 papers chosen from the papers evaluated in phase 1, stratified by animal and by country i.

This number was selected as an appropriately sized sub-sample of the papers assessed in phase 1 based, as was the case for phase 1, on the time necessary to complete the very detailed reports. The statistical methods and analysis of the papers were assessed to determine whether the experimental design and the statistical analysis were appropriate. This involved the expert judgement of two statisticians, both of whom assessed all 48 papers using the Quality of Experimental Design and Analysis checklist see Supporting Information S1.

The main experiment was the same as that analysed in phase 1. Errors of omission were noted. Any disagreements or differences in interpretation of the checklists were resolved by consultation and discussion with a third assessor and, where necessary, the relevant studies were re-analysed.

To allow for possible discrepancies between the two assessments, in phase 2 the mean of the results from the two statisticians are reported in all data summary tables. Overall agreement between the assessors was assessed once during each phase of the survey — In phase 1 both assessors applied the relevant checklist to the same sub-set of 30 of papers and their analyses compared, and in phase 2, all 48 papers were used to assess agreement see Figure 1. The NC3Rs gratefully acknowledges the invaluable expertise, advice, and support that all the contributors have given to this survey.

We would particularly like to acknowledge the help and expertise of the following people: information specialists Sue Spriggs, Diane Clay and Sam Vincent who performed the database searches, Karl Broman who was involved in data collection and statistical analysis phase 1 , Laura Playle who initially co-ordinated this project, Kathryn Chapman and Vicky Robinson both NC3Rs. Wrote the paper: CK. Browse Subject Areas? Click through the PLOS taxonomy to find articles in your field. Abstract For scientific, ethical and economic reasons, experiments involving animals should be appropriately designed, correctly analysed and transparently reported.

Introduction Scientific progress is driven by developing and testing novel hypotheses. Download: PPT. Table 1. Number of papers classified into general type of treatment procedure described in the study. Table 2. Number of studies reporting funding source classified by main funding body.

Quality of Reporting The survey's first question addressed the fundamental premise of each scientific publication. Table 3. Number of studies stating the purpose of the study in the introduction. Table 5. Number of studies that clearly identified the experimental unit. Table 6.

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Number of studies reporting the species or strain of the animals. Table 8. Number of studies reporting the age and weight of the animals. Table 9. Number of studies reporting animal numbers in the methods and results sections. Table Number of animals reported in methods and results sections for each study. Number of studies reporting the study hypothesis, three animal characteristics and the number of animals used.

Quality of Experimental Design Next we assessed the quality of experimental design, and in particular, how many papers had incorporated measures to reduce bias such as randomisation and blinding. Number of studies that reported using randomisation. Number of studies that used qualitative scores reporting blinding.