This article highlights the benefits of preregistration in improving the reliability and transparency of in vitro studies. By preregistering their studies, researchers can make their findings more reproducible, paving the way for medical progress, and accelerating the replacement of animal experiments.

The involvement of non-scientific staff in discussions about animal welfare and scientific quality is essential for biomedical research progress. In this study, we developed a survey to collect the self-perception of animal care staff (ACS) and laboratory technicians about their involvement in scientific planning and conduct. Participants were contacted to complete an anonymous online questionnaire. We obtained 850 responses, mainly from Europe: 564 from ACS and 286 from laboratory technicians. Job satisfaction was assessed as positive by ACS and laboratory technicians despite the low frequency of culture of care activities and mental health meetings. Both groups expressed their desire to be trained in research planning and conduct; however, regular training was not reported. In addition, the inability to act on animal welfare concerns owing to experimental reasons was reported by both groups. Over half of the participants felt valued and appreciated by the lead scientists or animal facility manager; however, it is not clear how they are acknowledged, as their names on the authors list or in the manuscript acknowledgments are barely included. Our results indicated that involvement of ACS and laboratory technicians in planning and conducting studies would improve their understanding of how experiments are done, and therefore communication processes, work satisfaction, animal welfare, and scientific quality. Finally, we provided recommendations to improve the engagement of ACS and laboratory technicians in discussions about animal research planning and conduct.

Extracting the research goal of a publication can potentially support researchers when searching the biomedical literature. Systems can make use of this information for various tasks, e.g., query processing or matching and ranking the candidates. However, this is a very subjective and complex task, which might involve various semantic types and may vary depending on the research area. Previous work have ventured in this area, but as far as we know, no specific dataset is yet available. We reused seven reviews from the European Commission with annotations about the research goal for more than 2.8k articles. We compiled the RG4C dataset, which we then used to fine tune a model for the automatic extraction of four criteria: “Field of Application”, “Disease Area”, “Disease Feature”, and “Biological Endpoint”. We obtained an overall f-score of 0.59, with results for each criterion ranging from 0.35 to 0.83. The RG4C dataset is available at: . Our source code is available at: ### Competing Interest Statement The authors have declared no competing interest.

We organized the SMAFIRA Shared in the scope of the BioNLP'2025 Workshop. Given two articles, our goal was to collect annotations about the similarity of their research goal. The test sets consisted of a list of reference articles and their corresponding top 20 similar articles from PubMed. The task consisted in annotating the similar articles regarding the similarity of their research goal with respect to the one from the corresponding reference article. The assessment of the similarity was based on three labels: "similar", "uncertain", or "not similar". We released two batches of test sets: (a) a first batch of 25 reference articles for five diseases; and (b) a second batch of 80 reference articles for 16 diseases. We collected manual annotations from two teams (RCX and Bf3R) and automatic predictions from two large language models (GPT-4omini and Llama3.3). The preliminary evaluation showed a rather low agreement between the annotators, however, some pairs could potentially be part of a future dataset.

The search for 3R-relevant information is a prerequisite for any planned experimental approach considering animal use. Such a literature search includes all methods to replace, reduce and refine (3Rs) animal testing with the aim of improving animal welfare, and requires an intensive screening of literature databases reflecting the current state of knowledge in experimental biomedicine. We developed SMAFIRA, a freely available online tool to facilitate the screening of PubMed/MEDLINE for possible alternatives to animal testing. SMAFIRA employs state-of-the-art language models from the field of deep learning, and provides relevant literature citations in a ranked order, classified according to the experimental model used. By using this classification, the search for alternative methods in the biomedical literature will become much more efficient. The tool is available at https://smafira.bf3r.de.

The translation of animal-based biomedical research into clinical research is often inadequate. Maximizing translation should be central to animal research on human diseases, guiding researchers in study design and animal model selection. However, practical considerations often drive the choice of animal model, which may not always reflect key patient characteristics, such as sex and age, impacting the disease's course. Despite diseases affecting both sexes, researchers frequently use male mice. To address this imbalance, journals and funding agencies have begun questioning the sex of animals used in studies and issued new guidelines. Conversely, the age of rodents is rarely discussed, even though many diseases primarily affect older patients. Young mice are commonly used, even in studies of diseases affecting older adults. Systematic comparisons between the age of rodents used and the age of patients in clinical trials are lacking. In this review, we systematically analyze the age and sex of mice used to model the five leading causes of global disability-adjusted life-years over the age of 75. We compare the results with the age and sex of patients in clinical trials focusing on Alzheimer's disease, stroke, type 2 diabetes mellitus, ischemic heart disease, and chronic obstructive pulmonary disease. We also analyze whether the age of the mice used has changed over the past decade. By systematically assessing the age and sex of the mice, we aim to initiate a discussion on the appropriate choice of animal model to improve the translatability of research results.

Current animal protection laws require replacement of animal experiments with alternative methods, whenever such methods are suitable to reach the intended scientific objective. However, searching for alternative methods in the scientific literature is a time-consuming task that requires careful screening of an enormously large number of experimental biomedical publications. The identification of potentially relevant methods, e.g. organ or cell culture models, or computer simulations, can be supported with text mining tools specifically built for this purpose. Such tools are trained (or fine tuned) on relevant data sets labeled by human experts. We developed the GoldHamster corpus, composed of 1,600 PubMed (Medline) articles (titles and abstracts), in which we manually identified the used experimental model according to a set of eight labels, namely: "in vivo", "organs", "primary cells", "immortal cell lines", "invertebrates", "humans", "in silico" and "other" (models). We recruited 13 annotators with expertise in the biomedical domain and assigned each article to two individuals. Four additional rounds of annotation aimed at improving the quality of the annotations with disagreements in the first round. Furthermore, we conducted various machine learning experiments based on supervised learning to evaluate the corpus for our classification task. We obtained more than 7,000 document-level annotations for the above labels. After the first round of annotation, the inter-annotator agreement (kappa coefficient) varied among labels, and ranged from 0.42 (for "others") to 0.82 (for "invertebrates"), with an overall score of 0.62. All disagreements were resolved in the subsequent rounds of annotation. The best-performing machine learning experiment used the PubMedBERT pre-trained model with fine-tuning to our corpus, which gained an overall f-score of 0.83. We obtained a corpus with high agreement for all labels, and our evaluation demonstrated that our corpus is suitable for training reliable predictive models for automatic classification of biomedical literature according to the used experimental models. Our SMAFIRA - "Smart feature-based interactive" - search tool ( https://smafira.bf3r.de ) will employ this classifier for supporting the retrieval of alternative methods to animal experiments. The corpus is available for download ( https://doi.org/10.5281/zenodo.7152295 ), as well as the source code ( https://github.com/mariananeves/goldhamster ) and the model ( https://huggingface.co/SMAFIRA/goldhamster ).

Chapter 37 was previously published non-open access. It has now been changed to open access under a CC BY 4.0 license and the copyright holder updated to ‘The Author(s)’. The book has also been updated with this change.

To meet regulatory requirements and the political pressure to minimize the number of animals used in research, it is critical to reduce the production of surplus animals.

The use of seed articles in information retrieval provides many advantages, such as a longer context and more details about the topic being searched for.Given a seed article (i.e., a PMID), PubMed provides a pre-compiled list of similar articles to support the user in finding equivalent papers in the biomedical literature.We aimed at performing a quantitative evaluation of the PubMed Similar Articles based on three existing biomedical text similarity datasets, namely, RELISH, TREC-COVID, and SMAFIRA-c.Further, we carried out a survey and an evaluation of various text similarity methods on these three datasets.Our experiments considered the original title and abstract from PubMed as well as automatically detected sections and manually annotated relevant sentences.We provide an overview about which methods better perform for each dataset and compare them to the ranking in PubMed similar articles.While results varied considerably among the datasets, we were able to obtain a better performance than PubMed for all of them.Datasets and source codes are available at: https://github.com/mariananeves/reranking

ZusammenfassungDas Ziel der EU-Versuchstierrichtlinie 2010/63/EU ist es, einheitliche rechtliche Rahmenbedingungen für Tierversuche in allen EU-Mitgliedstaaten zu schaffen. Aufgrund eigenständiger mitgliedstaatlicher Umsetzung der EU-Versuchstierrichtlinie in das jeweilige nationale Versuchstierrecht können nationale Regelungen durchaus ein unterschiedlich hohes Tierschutzniveau aufweisen. Deutlich zeigt sich dies bei der Tötung von überzähligen Versuchstieren, die regelmäßig bei der notwendigen Zucht von Versuchstieren entstehen. Gem. 1 S. 2 TierSchG muss nach deutschem Tierschutzrecht bei jeder Tötung eines Tieres ein vernünftiger Grund vorliegen. Dieses Erfordernis bezieht sich uneingeschränkt auch auf Versuchstiere und zeigt sich in seiner konkreten Ausgestaltung als nationale Besonderheit des deutschen Versuchstierrechts im Vergleich zu anderen Mitgliedstaaten. Fehlt ein vernünftiger Grund im Rahmen der Tötung eines Tieres, kann dies auch strafrechtliche Konsequenzen gem. 17 Nr. 1 TierSchG nach sich ziehen. Mangels gefestigter Rechtsprechung im Versuchstierbereich muss bei der rechtlich gebotenen Auslegung zur Bestimmung des unbestimmten Rechtsbegriffs des vernünftigen Grundes die Rechtsprechung aus anderen Bereiches des Tierschutzrechts herangezogen und auf das Versuchstierrecht übertragen werden. Unter Heranziehung der aktuellsten Rechtsprechung des Bundesverwaltungsgerichts zur Tötung von männlichen Küken zeigt sich, wie schwierig sich eine solche Übertragung in der rechtswissenschaftlichen Praxis gestaltet. Eine mögliche Übertragung von Wertungen aus dem Nutztierbereich muss dabei aufgrund der Komplexität der versuchstierrechtlichen Materie stets den konkreten Einzelfall berücksichtigen und kann keinesfalls pauschal erfolgen.

Zusammenfassung Überzählige Versuchstiere lassen sich auch bei bester Versuchsplanung und sorgfältigstem Zuchtmanagement nicht vermeiden, da bei der Zucht von Versuchstieren regelmäßig Tiere entstehen, die aufgrund verschiedenster Kriterien im geplanten Tierversuch, für den sie ursprünglich gezüchtet wurden, nicht eingesetzt werden können. Insbesondere bei genetisch veränderten Tieren scheidet eine Vermittlung oder Weiterverwendung für andere Versuchszwecke oder als Futtertier regelmäßig aus. Viele Einrichtungen können diese überzähligen Tiere aufgrund fehlender Haltungskapazitäten auch nicht bis an ihr natürliches Lebensende halten. In der Praxis stellt sich daher die ethisch und rechtlich viel diskutierte Frage, ob überzählige Versuchstiere unter Annahme eines vernünftigen Grundes nach 1 S. 2 TierSchG getötet werden dürfen. Im Kern geht es dabei um die im Einzelfall stets vorzunehmende Abwägung des Tierschutzes gem. Art. 20a GG und der Wissenschaftsfreiheit gem. Art. 5 Abs. 3 GG. Der vorliegende Beitrag möchte insbesondere untersuchen, ob eine Verfütterung von überzähligen Versuchstieren und die Unmöglichkeit einer artgerechten Haltung unter Einbeziehung aktueller Rechtsprechung für sich genommen ausreichen können, um eine Tötung von überzähligen Versuchstieren aus vernünftigem Grund zu rechtfertigen.

To meet regulatory requirements and the political pressure to minimize the number of animals used in research, it is critical to reduce the production of surplus animals.

Journal of Veterinary Pharmacology and TherapeuticsVolume 46, Issue S1 p. 32-32 ORAL PRESENTATIONS O10 | The importance of preregistration for animal-based research First published: 11 June 2023 https://doi.org/10.1111/jvp.13176Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL No abstract is available for this article. Volume46, IssueS1Special Issue: 15th International Congress of the European Association for Veterinary Pharmacology and Toxicology held Bruges, Belgium, July 2–5, 2023June 2023Pages 32-32 RelatedInformation

Preregistration of studies is a recognized tool in clinical research to improve the quality and reporting of all gained results. In preclinical research, preregistration could boost the translation of published results into clinical breakthroughs. When studies rely on animal testing or form the basis of clinical trials, maximizing the validity and reliability of research outcomes becomes in addition an ethical obligation. Nevertheless, the implementation of preregistration in animal research is still slow. However, research institutions, funders, and publishers start valuing preregistration, and thereby level the way for its broader acceptance in the future. A total of 3 public registries, the OSF registry, preclinicaltrials.eu, and animalstudyregistry.org already encourage the preregistration of research involving animals. Here, they jointly declare common standards to make preregistration a valuable tool for better science. Registries should meet the following criteria: public accessibility, transparency in their financial sources, tracking of changes, and warranty and sustainability of data. Furthermore, registration templates should cover a minimum set of mandatory information and studies have to be uniquely identifiable. Finally, preregistered studies should be linked to any published outcome. To ensure that preregistration becomes a powerful instrument, publishers, funders, and institutions should refer to registries that fulfill these minimum standards.

Translational biomedical research relies on animal experiments and provides the underlying proof of practice for clinical trials, which places an increased duty of care on translational researchers to derive the maximum possible output from every experiment performed. The implementation of open science practices has the potential to initiate a change in research culture that could improve the transparency and quality of translational research in general, as well as increasing the audience and scientific reach of published research. However, open science has become a buzzword in the scientific community that can often miss mark when it comes to practical implementation. In this Essay, we provide a guide to open science practices that can be applied throughout the research process, from study design, through data collection and analysis, to publication and dissemination, to help scientists improve the transparency and quality of their work. As open science practices continue to evolve, we also provide an online toolbox of resources that we will update continually.

AbstractAttempts to replicate published studies have too often failed, and promising preclinical results could not be translated into clinical breakthroughs. Major causes for this lack of reproducibility are practical reasons such as selective reporting, poor study design, or insufficient method description. However, a rigid incentive system shaped by publishers, institutions, and funders intensifies the problem by favoring exciting results over robust ones. Poor quality of biomedical research not only slows down the scientific progress, it also represents an ethical issue. When animal experiments do not contribute to any knowledge gain, the justification for these experiments is not given, and animal lives are wasted. Preregistration of animal research, i.e., registration of the study protocol before the experiment has started, supports scientists in designing an excellent research study, prevents questionable scientific practices, and improves the reporting of all outcomes. With the online platform animalstudyregistry.org, scientists worldwide can now easily register their animal study and show their commitment to open science. To enable a broad uptake of preregistration into biomedical research, funders, publishers, and institutions need to acknowledge preregistration as an engagement for transparent and robust science.

Non-technical summaries of research projects allow tracking the numbers and purpose of animal experiments related to SARS-CoV2 research so as to provide greater transparency on animal use.

The scientific community widely discusses preregistration. The main idea of preregistration is being able to untangle the a priori hypothesis from the outcome-driven and exploratory analyses once the data is generated. Researchers can ensure neutrality towards their data and an objective evaluation of the study outcomes by cultivating a record of the study, starting with the study plan. This record is especially valuable during the peer review process by assisting publishers in retracing the hypothesis generation and data analysis. Researchers have a couple of options for sharing their methods, plans, statistical analyses, and results with publishers: as a study protocol in a public registry (database) or as a registered report in a journal. The content of a preregistered study depends on the requirements of the database or journal. It can range from detailed study and analysis protocols to a simplified documentation of the exploratory process of data collection without an explicit plan for data evaluation. Publishers’ confidence in the reproducibility of research findings grows the more comprehensively the experimental plan is documented a priori, including what the authors expect to find and what these findings will mean. Public registries can offer multiple advantages and, if supported by journals, open up preregistration to a broader range of researchers. The requirement by the International Committee of Medical Journal Editors that clinical trials need to be registered prior to publication was an important milestone for the acceptance of preregistration among clinical researchers. The adoption of similar strategies by journals in preclinical and fundamental […]